substitution minor allele frequency (MAF) submission details 251 Caucasian population panels 210 non-Caucasian population panels polyphen sift id snp_id gene locuslink id chromosome chromosome coordinate mRNA accession protein accession nucleotide amino acid UCSC strand subsnp_id population id population handle local population id population description total chromosomes genotyped MAF mean MAF stdev chromosomes genotyped number of submissions mean MAF stdev chromosomes genotyped number of submissions update build validation criterion prediction score number sequences aligned prediction score divergence score number sequences aligned grantham MIM number cytogenetic gene description 1 rs328 LPL 4023 8 19864004 NM_000237 NP_000228 C/G S474X plus 3173350 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 112 0.02 0.19 0.19 248 3 0.14 0.02 1546 3 123 "by cluster,freq" Probably damaging Intolerant radical 238600 8p22 lipoprotein lipase 2 rs328 LPL 4023 8 19864004 NM_000237 NP_000228 C/G S474X plus 10467174 1303 SEQUENOM CEPH CEPH (92) 92 0.36 0.19 0.19 248 3 0.14 0.02 1546 3 123 "by cluster,freq" Probably damaging Intolerant radical 238600 8p22 lipoprotein lipase 3 rs328 LPL 4023 8 19864004 NM_000237 NP_000228 C/G S474X plus 24648907 1371 PERLEGEN AFD_EUR_PANEL European American (24) 44 0.27 0.19 0.19 248 3 0.14 0.02 1546 3 123 "by cluster,freq" Probably damaging Intolerant radical 238600 8p22 lipoprotein lipase 4 rs662 PON1 5444 7 94582097 NM_000446 NP_000437 A/G Q192R minus 667 506 NCBI NIHPDR NIHPDR 180 0.48 0.33 0.1 942 7 0.4 0.03 4482 8 123 "by submitter,freq,cluster" Borderline 1.188 47 Tolerant 0.61 2.75 32 conservative 168820 7q21.3 paraoxonase 1 5 rs662 PON1 5444 7 94582097 NM_000446 NP_000437 A/G Q192R minus 4573 491 HU-CHINA CAU "Australian, Belgian, Canadian, English, Finnish, French, German and USA" 460 0.33 0.33 0.1 942 7 0.4 0.03 4482 8 123 "by submitter,freq,cluster" Borderline 1.188 47 Tolerant 0.61 2.75 32 conservative 168820 7q21.3 paraoxonase 1 6 rs662 PON1 5444 7 94582097 NM_000446 NP_000437 A/G Q192R minus 5111592 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.17 0.33 0.1 942 7 0.4 0.03 4482 8 123 "by submitter,freq,cluster" Borderline 1.188 47 Tolerant 0.61 2.75 32 conservative 168820 7q21.3 paraoxonase 1 7 rs662 PON1 5444 7 94582097 NM_000446 NP_000437 A/G Q192R minus 5111592 1303 SEQUENOM CEPH CEPH (92) 92 0.18 0.33 0.1 942 7 0.4 0.03 4482 8 123 "by submitter,freq,cluster" Borderline 1.188 47 Tolerant 0.61 2.75 32 conservative 168820 7q21.3 paraoxonase 1 8 rs662 PON1 5444 7 94582097 NM_000446 NP_000437 A/G Q192R minus 5586846 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.27 0.33 0.1 942 7 0.4 0.03 4482 8 123 "by submitter,freq,cluster" Borderline 1.188 47 Tolerant 0.61 2.75 32 conservative 168820 7q21.3 paraoxonase 1 9 rs662 PON1 5444 7 94582097 NM_000446 NP_000437 A/G Q192R minus 16338591 1120 WIPGA POP-WIPGA-12-05-2003 CORIELL Mixed 56 0.34 0.33 0.1 942 7 0.4 0.03 4482 8 123 "by submitter,freq,cluster" Borderline 1.188 47 Tolerant 0.61 2.75 32 conservative 168820 7q21.3 paraoxonase 1 10 rs662 PON1 5444 7 94582097 NM_000446 NP_000437 A/G Q192R minus 24194186 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.17 0.33 0.1 942 7 0.4 0.03 4482 8 123 "by submitter,freq,cluster" Borderline 1.188 47 Tolerant 0.61 2.75 32 conservative 168820 7q21.3 paraoxonase 1 11 rs671 ALDH2 217 12 110704486 NM_000690 NP_000681 A/G E504K plus 3177110 619 WICVAR MITOGPOP6 CORIELL Mixed 62 0.06 0.06 0 62 1 0.14 0.12 386 4 123 "by cluster,freq" Borderline 1.072 136 Potentially intolerant 0.06 2.82 145 moderately conservative 100650 12q24.2 aldehyde dehydrogenase 2 family (mitochondrial) 12 rs678 ITIH1 3697 3 52796021 NM_002215 NP_002206 A/T E585V plus 21978763 1303 SEQUENOM CEPH CEPH (92) 92 0.38 0.41 0.05 140 2 0.27 0.16 94 2 123 "by cluster,freq" Probably damaging 2.145 19 moderately radical 147270 3p21.2-p21.1 inter-alpha (globulin) inhibitor H1 13 rs678 ITIH1 3697 3 52796021 NM_002215 NP_002206 A/T E585V plus 24349616 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.46 0.41 0.05 140 2 0.27 0.16 94 2 123 "by cluster,freq" Probably damaging 2.145 19 moderately radical 147270 3p21.2-p21.1 inter-alpha (globulin) inhibitor H1 14 rs704 VTN 7448 17 23718988 NM_000638 NP_000629 C/T T400M minus 8443 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.48 0.47 0.02 421 4 0.29 0.2 130 2 121 "by doubleHit,freq,cluster" Benign 0.778 11 moderately conservative 193190 17q11 "vitronectin (serum spreading factor, somatomedin B, complement S-protein)" 15 rs704 VTN 7448 17 23718988 NM_000638 NP_000629 C/T T400M minus 1352184 782 TSC-CSHL WICGR6_CAUCASIAN_POOLED WICGR Caucasian (48) 96 0.45 0.47 0.02 421 4 0.29 0.2 130 2 121 "by doubleHit,freq,cluster" Benign 0.778 11 moderately conservative 193190 17q11 "vitronectin (serum spreading factor, somatomedin B, complement S-protein)" 16 rs704 VTN 7448 17 23718988 NM_000638 NP_000629 C/T T400M minus 3172312 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.43 0.47 0.02 421 4 0.29 0.2 130 2 121 "by doubleHit,freq,cluster" Benign 0.778 11 moderately conservative 193190 17q11 "vitronectin (serum spreading factor, somatomedin B, complement S-protein)" 17 rs704 VTN 7448 17 23718988 NM_000638 NP_000629 C/T T400M minus 3172312 1303 SEQUENOM CEPH CEPH (92) 91 0.47 0.47 0.02 421 4 0.29 0.2 130 2 121 "by doubleHit,freq,cluster" Benign 0.778 11 moderately conservative 193190 17q11 "vitronectin (serum spreading factor, somatomedin B, complement S-protein)" 18 rs1208 NAT2 10 8 18302596 NM_000015 NP_000006 A/G R268K plus 2323986 782 TSC-CSHL WICGR6_CAUCASIAN_POOLED WICGR Caucasian (48) 96 0.29 0.34 0.04 434 4 0.29 0.19 412 6 123 "by doubleHit,freq,cluster" Benign 0.474 32 conservative 243400 8p22 N-acetyltransferase 2 (arylamine N-acetyltransferase) 19 rs1208 NAT2 10 8 18302596 NM_000015 NP_000006 A/G R268K plus 2323986 1303 SEQUENOM CEPH CEPH (92) 92 0.35 0.34 0.04 434 4 0.29 0.19 412 6 123 "by doubleHit,freq,cluster" Benign 0.474 32 conservative 243400 8p22 N-acetyltransferase 2 (arylamine N-acetyltransferase) 20 rs1208 NAT2 10 8 18302596 NM_000015 NP_000006 A/G R268K plus 5586793 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.4 0.34 0.04 434 4 0.29 0.19 412 6 123 "by doubleHit,freq,cluster" Benign 0.474 32 conservative 243400 8p22 N-acetyltransferase 2 (arylamine N-acetyltransferase) 21 rs1208 NAT2 10 8 18302596 NM_000015 NP_000006 A/G R268K plus 24796685 1303 SEQUENOM CEPH CEPH (92) 184 0.35 0.34 0.04 434 4 0.29 0.19 412 6 123 "by doubleHit,freq,cluster" Benign 0.474 32 conservative 243400 8p22 N-acetyltransferase 2 (arylamine N-acetyltransferase) 22 rs1258 TAF1L 138474 9 32623119 NM_153809 NP_722516 A/G M820T plus 24810791 1303 SEQUENOM CEPH CEPH (92) 184 0.06 0.06 0 184 1 123 "by cluster,freq" Benign 0.273 13 Tolerant 1 3.03 30 moderately conservative 607798 9p13.3 "TAF1-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa" 23 rs1303 SERPINA1 5265 14 93914596 NM_000295 NP_000286 G/T E400D plus 8326 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.3 0.29 0.05 366 4 0.28 0.03 1590 4 123 "by doubleHit,submitter,freq,cluster" Benign 0.079 58 Tolerant 1 2.76 77 conservative 107400 14q32.1 "serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1" 24 rs1303 SERPINA1 5265 14 93914596 NM_000295 NP_000286 G/T E400D plus 20190 523 WIAF-CSNP WIAF-CSNP-MITOGPOP4 "Europeans (20), Asians (10) and African-Americans (10)" 38 0.33 0.29 0.05 366 4 0.28 0.03 1590 4 123 "by doubleHit,submitter,freq,cluster" Benign 0.079 58 Tolerant 1 2.76 77 conservative 107400 14q32.1 "serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1" 25 rs1303 SERPINA1 5265 14 93914596 NM_000295 NP_000286 G/T E400D plus 16651029 1303 SEQUENOM CEPH CEPH (92) 92 0.3 0.29 0.05 366 4 0.28 0.03 1590 4 123 "by doubleHit,submitter,freq,cluster" Benign 0.079 58 Tolerant 1 2.76 77 conservative 107400 14q32.1 "serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1" 26 rs1303 SERPINA1 5265 14 93914596 NM_000295 NP_000286 G/T E400D plus 24129831 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.19 0.29 0.05 366 4 0.28 0.03 1590 4 123 "by doubleHit,submitter,freq,cluster" Benign 0.079 58 Tolerant 1 2.76 77 conservative 107400 14q32.1 "serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1" 27 rs1716 ITGAE 3682 17 3579585 NM_002208 NP_002199 C/T R950W minus 21376295 1303 SEQUENOM CEPH CEPH (92) 92 0.4 0.4 0 92 1 121 "by submitter,freq,cluster" Benign 0.9 5 Intolerant 0.02 2.83 18 moderately radical 604682 17p13 "integrin, alpha E (antigen CD103, human mucosal lymphocyte antigen 1; alpha polypeptide)" 28 rs1921 G1P2 9636 1 989675 NM_005101 NP_005092 A/G S83N plus 24810939 1303 SEQUENOM CEPH CEPH (92) 184 0.37 0.37 0 184 1 0.2 0 10 1 123 "by cluster,freq" Benign 0.03 5 Potentially intolerant 0.07 2.9 385 conservative 147571 1p36.33 "interferon, alpha-inducible protein (clone IFI-15K)" 29 rs2240 MKI67 4288 10 129797534 NM_002417 NP_002408 C/G L854V plus 2960666 1303 SEQUENOM CEPH CEPH (92) 92 0.25 0.24 0.03 140 2 0.28 0.05 104 3 123 "by doubleHit,freq,cluster" conservative 176741 10q25-qter antigen identified by monoclonal antibody Ki-67 30 rs2240 MKI67 4288 10 129797534 NM_002417 NP_002408 C/G L854V plus 23644026 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.24 0.03 140 2 0.28 0.05 104 3 123 "by doubleHit,freq,cluster" conservative 176741 10q25-qter antigen identified by monoclonal antibody Ki-67 31 rs2347 POLR3E 55718 16 22227018 NM_018119 NP_060589 A/C S46A minus 2375 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.08 0.08 0.02 260 3 123 "HapMap,submitter,freq" Borderline 1.163 11 Tolerant 0.58 2.85 24 moderately conservative 16p12.3 polymerase (RNA) III (DNA directed) polypeptide E (80kD) 32 rs2347 POLR3E 55718 16 22227018 NM_018119 NP_060589 A/C S46A minus 2375 1303 SEQUENOM CEPH CEPH (92) 92 0.09 0.08 0.02 260 3 123 "HapMap,submitter,freq" Borderline 1.163 11 Tolerant 0.58 2.85 24 moderately conservative 16p12.3 polymerase (RNA) III (DNA directed) polypeptide E (80kD) 33 rs2347 POLR3E 55718 16 22227018 NM_018119 NP_060589 A/C S46A minus 24569247 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.08 0.02 260 3 123 "HapMap,submitter,freq" Borderline 1.163 11 Tolerant 0.58 2.85 24 moderately conservative 16p12.3 polymerase (RNA) III (DNA directed) polypeptide E (80kD) 34 rs2640 HRI 27102 7 5839691 NM_014413 NP_055228 C/T K558R plus 2670 885 TSC-CSHL HapMap-CEPH-30-trios 110 0.03 0.08 0.04 916 6 0.33 0.04 4106 4 123 "HapMap,freq,cluster" Borderline 1.047 8 Tolerant 0.27 2.99 11 conservative 7p22 heme-regulated initiation factor 2-alpha kinase 35 rs2640 HRI 27102 7 5839691 NM_014413 NP_055228 C/T K558R plus 2670 1303 SEQUENOM CEPH CEPH (92) 92 0.09 0.08 0.04 916 6 0.33 0.04 4106 4 123 "HapMap,freq,cluster" Borderline 1.047 8 Tolerant 0.27 2.99 11 conservative 7p22 heme-regulated initiation factor 2-alpha kinase 36 rs2640 HRI 27102 7 5839691 NM_014413 NP_055228 C/T K558R plus 4551 491 HU-CHINA CAU "Australian, Belgian, Canadian, English, Finnish, French, German and USA" 460 0.11 0.08 0.04 916 6 0.33 0.04 4106 4 123 "HapMap,freq,cluster" Borderline 1.047 8 Tolerant 0.27 2.99 11 conservative 7p22 heme-regulated initiation factor 2-alpha kinase 37 rs2640 HRI 27102 7 5839691 NM_014413 NP_055228 C/T K558R plus 16336055 902 AFFY Caucasian 22 0.09 0.08 0.04 916 6 0.33 0.04 4106 4 123 "HapMap,freq,cluster" Borderline 1.047 8 Tolerant 0.27 2.99 11 conservative 7p22 heme-regulated initiation factor 2-alpha kinase 38 rs2640 HRI 27102 7 5839691 NM_014413 NP_055228 C/T K558R plus 23989050 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.08 0.04 916 6 0.33 0.04 4106 4 123 "HapMap,freq,cluster" Borderline 1.047 8 Tolerant 0.27 2.99 11 conservative 7p22 heme-regulated initiation factor 2-alpha kinase 39 rs2640 HRI 27102 7 5839691 NM_014413 NP_055228 C/T K558R plus 24796328 1303 SEQUENOM CEPH CEPH (92) 184 0.04 0.08 0.04 916 6 0.33 0.04 4106 4 123 "HapMap,freq,cluster" Borderline 1.047 8 Tolerant 0.27 2.99 11 conservative 7p22 heme-regulated initiation factor 2-alpha kinase 40 rs2759 MPO 4353 17 53703105 NM_000250 NP_000241 A/G I717V minus 16338615 1120 WIPGA POP-WIPGA-12-05-2003 CORIELL Mixed 16 0.06 0.03 0.02 64 2 0.04 0 46 1 123 "by cluster,freq" Benign 0.293 19 Tolerant 1 2.78 29 conservative 606989 17q23.1 myeloperoxidase 41 rs2759 MPO 4353 17 53703105 NM_000250 NP_000241 A/G I717V minus 23791841 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.03 0.02 64 2 0.04 0 46 1 123 "by cluster,freq" Benign 0.293 19 Tolerant 1 2.78 29 conservative 606989 17q23.1 myeloperoxidase 42 rs2791 TRAP1 10131 16 3648171 NM_016292 NP_057376 C/T R692H plus 2821 1303 SEQUENOM CEPH CEPH (92) 92 0.09 0.08 0.02 140 2 123 "by cluster,freq" Potentially damaging 1.355 6 Intolerant 0.01 2.85 27 conservative 606219 16p13.3 heat shock protein 75 43 rs2791 TRAP1 10131 16 3648171 NM_016292 NP_057376 C/T R692H plus 24709278 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.08 0.02 140 2 123 "by cluster,freq" Potentially damaging 1.355 6 Intolerant 0.01 2.85 27 conservative 606219 16p13.3 heat shock protein 75 44 rs2941 GRM1 2911 6 146796825 NM_000838 NP_000829 A/G V929I plus 2972 549 KYUGEN CP CEPH (78) 156 0.11 0.09 0.02 432 3 123 "by cluster,freq" Benign 0.238 16 conservative 604473 6q24 "glutamate receptor, metabotropic 1" 45 rs2941 GRM1 2911 6 146796825 NM_000838 NP_000829 A/G V929I plus 14796794 1303 SEQUENOM CEPH CEPH (92) 92 0.07 0.09 0.02 432 3 123 "by cluster,freq" Benign 0.238 16 conservative 604473 6q24 "glutamate receptor, metabotropic 1" 46 rs2941 GRM1 2911 6 146796825 NM_000838 NP_000829 A/G V929I plus 24796320 1303 SEQUENOM CEPH CEPH (92) 184 0.09 0.09 0.02 432 3 123 "by cluster,freq" Benign 0.238 16 conservative 604473 6q24 "glutamate receptor, metabotropic 1" 47 rs3501 PAXIP1L 22976 7 154176057 NM_007349 NP_031375 A/G M979V minus 3536 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.26 0.26 0 212 2 0.4 0 10 1 100 "HapMap,submitter,freq,cluster" conservative 608254 7q36 PAX transcription activation domain interacting protein 1 like 48 rs3501 PAXIP1L 22976 7 154176057 NM_007349 NP_031375 A/G M979V minus 3536 1303 SEQUENOM CEPH CEPH (92) 92 0.26 0.26 0 212 2 0.4 0 10 1 100 "HapMap,submitter,freq,cluster" conservative 608254 7q36 PAX transcription activation domain interacting protein 1 like 49 rs3575 LDHB 3945 12 21679867 NM_002300 NP_002291 C/T C294Y plus 24811306 1303 SEQUENOM CEPH CEPH (92) 184 0.41 0.41 0 184 1 123 "by cluster,freq" Probably damaging 3.442 150 Intolerant 0 2.84 161 radical 150100 12p12.2-p12.1 lactate dehydrogenase B 50 rs4530 ADORA2A 135 22 23154075 NM_000675 NP_000666 C/T A50V plus 7888 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 74 0.03 0.03 0 74 1 0.05 0.01 126 2 123 "HapMap,freq,cluster" Benign 0.173 9 Tolerant 1 2.77 49 moderately conservative 102776 22q11.23 adenosine A2a receptor 51 rs4531 DBH 1621 9 133538924 NM_000787 NP_000778 G/T A304S plus 7897 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 70 0.1 0.09 0.01 162 2 0.07 0.02 574 3 121 "by cluster,freq" Borderline 1.07 11 Tolerant 0.9 2.81 27 moderately conservative 223360 9q34 dopamine beta-hydroxylase (dopamine beta-monooxygenase) 52 rs4531 DBH 1621 9 133538924 NM_000787 NP_000778 G/T A304S plus 22887000 1303 SEQUENOM CEPH CEPH (92) 92 0.09 0.09 0.01 162 2 0.07 0.02 574 3 121 "by cluster,freq" Borderline 1.07 11 Tolerant 0.9 2.81 27 moderately conservative 223360 9q34 dopamine beta-hydroxylase (dopamine beta-monooxygenase) 53 rs4534 CYP11B1 1584 8 143958104 NM_000497 NP_000488 A/G R43Q minus 8040 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 86 0.1 0.1 0 86 1 0.4 0.13 1448 4 123 "by doubleHit,freq,cluster" conservative 202010 8q21 "cytochrome P450, family 11, subfamily B, polypeptide 1" 54 rs4539 CYP11B2 1585 8 143993541 NM_000498 NP_000489 A/G K173R minus 8079 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 86 0.33 0.33 0 86 1 0.3 0 148 1 52 "by cluster,freq" Tolerant 0.55 2.81 33 conservative 124080 8q21-q22 "cytochrome P450, family 11, subfamily B, polypeptide 2" 55 rs4541 CYP11B1 1584 8 143953695 NM_000497 NP_000488 C/T A386V minus 8047 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 86 0.33 0.33 0 172 2 0.1 0 68 1 120 "by doubleHit,freq,cluster" Possibly damaging 1.505 36 moderately conservative 202010 8q21 "cytochrome P450, family 11, subfamily B, polypeptide 1" 56 rs4541 CYP11B1 1584 8 143953695 NM_000497 NP_000488 C/T A386V minus 8084 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 86 0.33 0.33 0 172 2 0.1 0 68 1 120 "by doubleHit,freq,cluster" Possibly damaging 1.505 36 moderately conservative 202010 8q21 "cytochrome P450, family 11, subfamily B, polypeptide 1" 57 rs4544 CYP11B2 1585 8 143991808 NM_000498 NP_000489 C/T I339T minus 8088 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 80 0.33 0.33 0 80 1 0.45 0.07 82 2 123 "by cluster,freq" Benign 0.225 36 Tolerant 0.52 2.81 33 moderately conservative 124080 8q21-q22 "cytochrome P450, family 11, subfamily B, polypeptide 2" 58 rs4545 CYP11B2 1585 8 143991043 NM_000498 NP_000489 A/G G435S minus 8089 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 82 0.33 0.33 0 82 1 0.05 0 68 1 120 "by doubleHit,freq,cluster" Potentially damaging 1.38 17 Tolerant 0.66 2.84 27 moderately conservative 124080 8q21-q22 "cytochrome P450, family 11, subfamily B, polypeptide 2" 59 rs4562 CLDN7 1366 17 7104463 NM_001307 NP_001298 A/G V197A plus 8465 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.32 0.32 0 280 2 120 "by doubleHit,freq,cluster" Benign 0.847 27 moderately conservative 17p13 claudin 7 60 rs4562 CLDN7 1366 17 7104463 NM_001307 NP_001298 A/G V197A plus 606039 1303 SEQUENOM CEPH CEPH (92) 92 0.32 0.32 0 280 2 120 "by doubleHit,freq,cluster" Benign 0.847 27 moderately conservative 17p13 claudin 7 61 rs4588 GC 2638 4 72983358 NM_000583 NP_000574 A/C T436K minus 8817 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.3 0.33 0.07 524 4 0.22 0.04 344 4 123 "by cluster,freq" Benign 0.198 9 Borderline 0.16 2.75 20 moderately conservative 139200 4q12-q13 group-specific component (vitamin D binding protein) 62 rs4588 GC 2638 4 72983358 NM_000583 NP_000574 A/C T436K minus 6903803 775 SNP500CANCER CAUC1 Caucasian (31) 60 0.23 0.33 0.07 524 4 0.22 0.04 344 4 123 "by cluster,freq" Benign 0.198 9 Borderline 0.16 2.75 20 moderately conservative 139200 4q12-q13 group-specific component (vitamin D binding protein) 63 rs4588 GC 2638 4 72983358 NM_000583 NP_000574 A/C T436K minus 6903803 1303 SEQUENOM CEPH CEPH (92) 92 0.3 0.33 0.07 524 4 0.22 0.04 344 4 123 "by cluster,freq" Benign 0.198 9 Borderline 0.16 2.75 20 moderately conservative 139200 4q12-q13 group-specific component (vitamin D binding protein) 64 rs4588 GC 2638 4 72983358 NM_000583 NP_000574 A/C T436K minus 24796216 1303 SEQUENOM CEPH CEPH (92) 184 0.4 0.33 0.07 524 4 0.22 0.04 344 4 123 "by cluster,freq" Benign 0.198 9 Borderline 0.16 2.75 20 moderately conservative 139200 4q12-q13 group-specific component (vitamin D binding protein) 65 rs4602 KRT19 3880 17 36937847 NM_002276 NP_002267 C/G A60G minus 8962 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.37 0.34 0.06 324 3 0.15 0.17 86 2 123 "by doubleHit,freq" Tolerant 0.65 2.87 65 moderately conservative 148020 17q21.2 keratin 19 66 rs4602 KRT19 3880 17 36937847 NM_002276 NP_002267 C/G A60G minus 8962 1303 SEQUENOM CEPH CEPH (92) 92 0.34 0.34 0.06 324 3 0.15 0.17 86 2 123 "by doubleHit,freq" Tolerant 0.65 2.87 65 moderately conservative 148020 17q21.2 keratin 19 67 rs4602 KRT19 3880 17 36937847 NM_002276 NP_002267 C/G A60G minus 23597995 1371 PERLEGEN AFD_EUR_PANEL European American (24) 44 0.23 0.34 0.06 324 3 0.15 0.17 86 2 123 "by doubleHit,freq" Tolerant 0.65 2.87 65 moderately conservative 148020 17q21.2 keratin 19 68 rs4619 IGFBP1 3484 7 45705909 NM_000596 NP_000587 A/G I253M plus 9319 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.36 0.34 0.03 628 5 0.4 0.08 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.88 12 Borderline 0.2 2.8 26 conservative 146730 7p13-p12 insulin-like growth factor binding protein 1 69 rs4619 IGFBP1 3484 7 45705909 NM_000596 NP_000587 A/G I253M plus 2965913 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.3 0.34 0.03 628 5 0.4 0.08 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.88 12 Borderline 0.2 2.8 26 conservative 146730 7p13-p12 insulin-like growth factor binding protein 1 70 rs4619 IGFBP1 3484 7 45705909 NM_000596 NP_000587 A/G I253M plus 2965913 1303 SEQUENOM CEPH CEPH (92) 92 0.36 0.34 0.03 628 5 0.4 0.08 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.88 12 Borderline 0.2 2.8 26 conservative 146730 7p13-p12 insulin-like growth factor binding protein 1 71 rs4619 IGFBP1 3484 7 45705909 NM_000596 NP_000587 A/G I253M plus 13452540 693 EGP_SNPS PDR90 NIHPDR 180 0.35 0.34 0.03 628 5 0.4 0.08 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.88 12 Borderline 0.2 2.8 26 conservative 146730 7p13-p12 insulin-like growth factor binding protein 1 72 rs4619 IGFBP1 3484 7 45705909 NM_000596 NP_000587 A/G I253M plus 23455231 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.29 0.34 0.03 628 5 0.4 0.08 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.88 12 Borderline 0.2 2.8 26 conservative 146730 7p13-p12 insulin-like growth factor binding protein 1 73 rs4644 LGALS3 3958 14 54674688 NM_002306 NP_002297 A/C P64H plus 9801 1303 SEQUENOM CEPH CEPH (92) 92 0.08 0.21 0.25 138 2 0.22 0.11 86 2 123 "by cluster,freq" moderately conservative 153619 14q21-q22 "lectin, galactoside-binding, soluble, 3 (galectin 3)" 74 rs4644 LGALS3 3958 14 54674688 NM_002306 NP_002297 A/C P64H plus 24615984 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.46 0.21 0.25 138 2 0.22 0.11 86 2 123 "by cluster,freq" moderately conservative 153619 14q21-q22 "lectin, galactoside-binding, soluble, 3 (galectin 3)" 75 rs4652 LGALS3 3958 14 54674789 NM_002306 NP_002297 A/C T98P plus 10155 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.45 0.46 0.03 280 2 120 "by doubleHit,freq,cluster" conservative 153619 14q21-q22 "lectin, galactoside-binding, soluble, 3 (galectin 3)" 76 rs4652 LGALS3 3958 14 54674789 NM_002306 NP_002297 A/C T98P plus 10741054 1303 SEQUENOM CEPH CEPH (92) 92 0.49 0.46 0.03 280 2 120 "by doubleHit,freq,cluster" conservative 153619 14q21-q22 "lectin, galactoside-binding, soluble, 3 (galectin 3)" 77 rs4660 SPP1 6696 4 89261184 NM_000582 NP_000573 A/G R287H plus 10351 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.13 0.13 0 280 2 0.17 0 46 1 123 by freq Possibly damaging 1.979 20 conservative 166490 4q21-q25 "secreted phosphoprotein 1 (osteopontin, bone sialoprotein I, early T-lymphocyte activation 1)" 78 rs4660 SPP1 6696 4 89261184 NM_000582 NP_000573 A/G R287H plus 10351 1303 SEQUENOM CEPH CEPH (92) 92 0.13 0.13 0 280 2 0.17 0 46 1 123 by freq Possibly damaging 1.979 20 conservative 166490 4q21-q25 "secreted phosphoprotein 1 (osteopontin, bone sialoprotein I, early T-lymphocyte activation 1)" 79 rs4673 CYBA 1535 16 87240737 NM_000101 NP_000092 C/T Y72H minus 9045 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.5 0.42 0.09 506 6 0.13 0.11 1918 7 123 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.704 16 moderately conservative 608508 16q24 "cytochrome b-245, alpha polypeptide" 80 rs4673 CYBA 1535 16 87240737 NM_000101 NP_000092 C/T Y72H minus 3173156 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 44 0.43 0.42 0.09 506 6 0.13 0.11 1918 7 123 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.704 16 moderately conservative 608508 16q24 "cytochrome b-245, alpha polypeptide" 81 rs4673 CYBA 1535 16 87240737 NM_000101 NP_000092 C/T Y72H minus 6598678 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.34 0.42 0.09 506 6 0.13 0.11 1918 7 123 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.704 16 moderately conservative 608508 16q24 "cytochrome b-245, alpha polypeptide" 82 rs4673 CYBA 1535 16 87240737 NM_000101 NP_000092 C/T Y72H minus 6598678 1303 SEQUENOM CEPH CEPH (92) 46 0.5 0.42 0.09 506 6 0.13 0.11 1918 7 123 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.704 16 moderately conservative 608508 16q24 "cytochrome b-245, alpha polypeptide" 83 rs4673 CYBA 1535 16 87240737 NM_000101 NP_000092 C/T Y72H minus 6903734 775 SNP500CANCER CAUC1 Caucasian (31) 60 0.32 0.42 0.09 506 6 0.13 0.11 1918 7 123 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.704 16 moderately conservative 608508 16q24 "cytochrome b-245, alpha polypeptide" 84 rs4673 CYBA 1535 16 87240737 NM_000101 NP_000092 C/T Y72H minus 23779281 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.33 0.42 0.09 506 6 0.13 0.11 1918 7 123 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.704 16 moderately conservative 608508 16q24 "cytochrome b-245, alpha polypeptide" 85 rs4740 EBI3 10148 19 4187996 NM_005755 NP_005746 A/G V201I plus 13009 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.41 0.35 0.07 556 6 0.31 0.03 136 4 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 1 2.84 19 conservative 605816 19p13.3 Epstein-Barr virus induced gene 3 86 rs4740 EBI3 10148 19 4187996 NM_005755 NP_005746 A/G V201I plus 88814 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 20 0.25 0.35 0.07 556 6 0.31 0.03 136 4 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 1 2.84 19 conservative 605816 19p13.3 Epstein-Barr virus induced gene 3 87 rs4740 EBI3 10148 19 4187996 NM_005755 NP_005746 A/G V201I plus 88814 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 88 0.28 0.35 0.07 556 6 0.31 0.03 136 4 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 1 2.84 19 conservative 605816 19p13.3 Epstein-Barr virus induced gene 3 88 rs4740 EBI3 10148 19 4187996 NM_005755 NP_005746 A/G V201I plus 1968400 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.3 0.35 0.07 556 6 0.31 0.03 136 4 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 1 2.84 19 conservative 605816 19p13.3 Epstein-Barr virus induced gene 3 89 rs4740 EBI3 10148 19 4187996 NM_005755 NP_005746 A/G V201I plus 1968400 1303 SEQUENOM CEPH CEPH (92) 92 0.41 0.35 0.07 556 6 0.31 0.03 136 4 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 1 2.84 19 conservative 605816 19p13.3 Epstein-Barr virus induced gene 3 90 rs4740 EBI3 10148 19 4187996 NM_005755 NP_005746 A/G V201I plus 24191234 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.29 0.35 0.07 556 6 0.31 0.03 136 4 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 1 2.84 19 conservative 605816 19p13.3 Epstein-Barr virus induced gene 3 91 rs4760 PLAUR 5329 19 48844940 NM_002659 NP_002650 C/T L317P minus 10984 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.11 0.13 0.03 510 4 0.02 0 46 1 121 "by doubleHit,freq,cluster" Possibly damaging 1.947 9 moderately conservative 173391 19q13 "plasminogen activator, urokinase receptor" 92 rs4760 PLAUR 5329 19 48844940 NM_002659 NP_002650 C/T L317P minus 13784 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.16 0.13 0.03 510 4 0.02 0 46 1 121 "by doubleHit,freq,cluster" Possibly damaging 1.947 9 moderately conservative 173391 19q13 "plasminogen activator, urokinase receptor" 93 rs4760 PLAUR 5329 19 48844940 NM_002659 NP_002650 C/T L317P minus 5607654 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 42 0.12 0.13 0.03 510 4 0.02 0 46 1 121 "by doubleHit,freq,cluster" Possibly damaging 1.947 9 moderately conservative 173391 19q13 "plasminogen activator, urokinase receptor" 94 rs4760 PLAUR 5329 19 48844940 NM_002659 NP_002650 C/T L317P minus 21508716 1303 SEQUENOM CEPH CEPH (92) 92 0.14 0.13 0.03 510 4 0.02 0 46 1 121 "by doubleHit,freq,cluster" Possibly damaging 1.947 9 moderately conservative 173391 19q13 "plasminogen activator, urokinase receptor" 95 rs4774 MHC2TA 4261 16 10908349 NM_000246 NP_000237 C/G G500A plus 11869 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.36 0.33 0.04 698 6 0.18 0.11 94 2 123 "HapMap,doubleHit,freq,cluster" Borderline 1.227 9 moderately conservative 600005 16p13 MHC class II transactivator 96 rs4774 MHC2TA 4261 16 10908349 NM_000246 NP_000237 C/G G500A plus 14168 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.31 0.33 0.04 698 6 0.18 0.11 94 2 123 "HapMap,doubleHit,freq,cluster" Borderline 1.227 9 moderately conservative 600005 16p13 MHC class II transactivator 97 rs4774 MHC2TA 4261 16 10908349 NM_000246 NP_000237 C/G G500A plus 3172899 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 62 0.39 0.33 0.04 698 6 0.18 0.11 94 2 123 "HapMap,doubleHit,freq,cluster" Borderline 1.227 9 moderately conservative 600005 16p13 MHC class II transactivator 98 rs4774 MHC2TA 4261 16 10908349 NM_000246 NP_000237 C/G G500A plus 6596713 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.32 0.33 0.04 698 6 0.18 0.11 94 2 123 "HapMap,doubleHit,freq,cluster" Borderline 1.227 9 moderately conservative 600005 16p13 MHC class II transactivator 99 rs4774 MHC2TA 4261 16 10908349 NM_000246 NP_000237 C/G G500A plus 6596713 1303 SEQUENOM CEPH CEPH (92) 92 0.36 0.33 0.04 698 6 0.18 0.11 94 2 123 "HapMap,doubleHit,freq,cluster" Borderline 1.227 9 moderately conservative 600005 16p13 MHC class II transactivator 100 rs4774 MHC2TA 4261 16 10908349 NM_000246 NP_000237 C/G G500A plus 23587538 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.23 0.33 0.04 698 6 0.18 0.11 94 2 123 "HapMap,doubleHit,freq,cluster" Borderline 1.227 9 moderately conservative 600005 16p13 MHC class II transactivator 101 rs4807 TXNDC7 10130 2 10881501 NM_005742 NP_005733 A/G K214R minus 15613 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.22 0.22 0 328 3 0.31 0.04 1586 3 123 "by doubleHit,freq,cluster" Potentially damaging 1.393 14 Borderline 0.19 2.9 29 conservative 2p25.1 thioredoxin domain containing 7 (protein disulfide isomerase) 102 rs4807 TXNDC7 10130 2 10881501 NM_005742 NP_005733 A/G K214R minus 2427777 1303 SEQUENOM CEPH CEPH (92) 92 0.22 0.22 0 328 3 0.31 0.04 1586 3 123 "by doubleHit,freq,cluster" Potentially damaging 1.393 14 Borderline 0.19 2.9 29 conservative 2p25.1 thioredoxin domain containing 7 (protein disulfide isomerase) 103 rs4807 TXNDC7 10130 2 10881501 NM_005742 NP_005733 A/G K214R minus 24162907 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.22 0 328 3 0.31 0.04 1586 3 123 "by doubleHit,freq,cluster" Potentially damaging 1.393 14 Borderline 0.19 2.9 29 conservative 2p25.1 thioredoxin domain containing 7 (protein disulfide isomerase) 104 rs4814 SRP14 6727 15 38115849 NM_003134 NP_003125 A/G T130A minus 15331 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.24 0.31 0.1 376 2 52 by freq moderately conservative 600708 15q22 signal recognition particle 14kDa (homologous Alu RNA binding protein) 105 rs4814 SRP14 6727 15 38115849 NM_003134 NP_003125 A/G T130A minus 15862 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.38 0.31 0.1 376 2 52 by freq moderately conservative 600708 15q22 signal recognition particle 14kDa (homologous Alu RNA binding protein) 106 rs4816 PCMT1 5110 6 150206859 NM_005389 NP_005380 A/G V120I plus 15904 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.37 0.37 0 188 1 108 by freq Benign 0.304 16 Tolerant 1 2.86 29 conservative 176851 6q24-q25 protein-L-isoaspartate (D-aspartate) O-methyltransferase 107 rs4870 TNFRSF14 8764 1 2528567 NM_003820 NP_003811 A/G K17R minus 16359043 693 EGP_SNPS PDR90 NIHPDR 172 0.42 0.42 0 172 1 120 "by doubleHit,freq,cluster" conservative 602746 1p36.3-p36.2 "tumor necrosis factor receptor superfamily, member 14 (herpesvirus entry mediator)" 108 rs4907 PSMB3 5691 17 34163025 NM_002795 NP_002786 A/T M34L plus 6616906 1303 SEQUENOM CEPH CEPH (92) 92 0.03 0.03 0 92 1 123 by freq Borderline 1.14 39 Intolerant 0.05 2.88 38 conservative 602176 17q12 "proteasome (prosome, macropain) subunit, beta type, 3" 109 rs4925 GSTO1 9446 10 106012779 NM_004832 NP_004823 A/C A140D plus 4926470 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.34 0.35 0.01 260 3 0.13 0.02 1620 4 123 "HapMap,submitter,freq,cluster" Benign 0.184 19 Borderline 0.16 2.93 23 moderately radical 605482 10q25.1 glutathione S-transferase omega 1 110 rs4925 GSTO1 9446 10 106012779 NM_004832 NP_004823 A/C A140D plus 20723413 1303 SEQUENOM CEPH CEPH (92) 92 0.36 0.35 0.01 260 3 0.13 0.02 1620 4 123 "HapMap,submitter,freq,cluster" Benign 0.184 19 Borderline 0.16 2.93 23 moderately radical 605482 10q25.1 glutathione S-transferase omega 1 111 rs4925 GSTO1 9446 10 106012779 NM_004832 NP_004823 A/C A140D plus 24502881 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.33 0.35 0.01 260 3 0.13 0.02 1620 4 123 "HapMap,submitter,freq,cluster" Benign 0.184 19 Borderline 0.16 2.93 23 moderately radical 605482 10q25.1 glutathione S-transferase omega 1 112 rs4945 MFGE8 4240 15 87257548 NM_005928 NP_005919 A/C R3S minus 5471 1303 SEQUENOM CEPH CEPH (92) 92 0.4 0.4 0 92 1 123 by freq moderately radical 602281 15q25 milk fat globule-EGF factor 8 protein 113 rs5054 AKR1B1 231 7 133601027 NM_001628 NP_001619 A/T I15F minus 6498 1303 SEQUENOM CEPH CEPH (92) 92 0.01 0.01 0 92 1 0.1 0 68 1 52 HapMap Possibly damaging 1.697 67 Intolerant 0.01 2.76 118 conservative 103880 7q35 "aldo-keto reductase family 1, member B1 (aldose reductase)" 114 rs5056 AKR1B1 231 7 133593702 NM_001628 NP_001619 A/T H42L minus 6500 1303 SEQUENOM CEPH CEPH (92) 92 0.01 0.01 0 92 1 0.05 0 80 1 52 by freq Probably damaging 3.801 71 Intolerant 0 2.77 123 moderately conservative 103880 7q35 "aldo-keto reductase family 1, member B1 (aldose reductase)" 115 rs5167 APOC4 346 19 50140305 NM_001646 NP_001637 G/T L96R plus 16797417 1303 SEQUENOM CEPH CEPH (92) 92 0.23 0.38 0.12 322 3 0.4 0.06 450 5 123 "by doubleHit,submitter,freq,cluster" moderately radical 600745 19q13.2 apolipoprotein C-IV 116 rs5167 APOC4 346 19 50140305 NM_001646 NP_001637 G/T L96R plus 24106807 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.39 0.38 0.12 322 3 0.4 0.06 450 5 123 "by doubleHit,submitter,freq,cluster" moderately radical 600745 19q13.2 apolipoprotein C-IV 117 rs5167 APOC4 346 19 50140305 NM_001646 NP_001637 G/T L96R plus 24795972 1303 SEQUENOM CEPH CEPH (92) 184 0.45 0.38 0.12 322 3 0.4 0.06 450 5 123 "by doubleHit,submitter,freq,cluster" moderately radical 600745 19q13.2 apolipoprotein C-IV 118 rs5273 PTGS2 5743 1 183375425 NM_000963 NP_000954 C/T V511A minus 4479801 506 NCBI NIHPDR NIHPDR 160 0.01 0.01 0 330 2 0.05 0.06 380 5 113 "by cluster,freq" Benign 0.282 62 Tolerant 0.54 2.88 54 moderately conservative 600262 1q25.2-q25.3 prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase) 119 rs5273 PTGS2 5743 1 183375425 NM_000963 NP_000954 C/T V511A minus 6396201 693 EGP_SNPS PDR90 NIHPDR 170 0.01 0.01 0 330 2 0.05 0.06 380 5 113 "by cluster,freq" Benign 0.282 62 Tolerant 0.54 2.88 54 moderately conservative 600262 1q25.2-q25.3 prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase) 120 rs5294 CYP11B1 1584 8 143953458 NM_000497 NP_000488 C/T Y439H minus 24796366 1303 SEQUENOM CEPH CEPH (92) 184 0.36 0.36 0 184 1 0.05 0 68 1 123 "by cluster,freq" Borderline 0.16 2.77 40 moderately conservative 202010 8q21 "cytochrome P450, family 11, subfamily B, polypeptide 1" 121 rs5320 DBH 1621 9 133537027 NM_000787 NP_000778 A/G A197T plus 6782 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.02 0.04 0.04 210 2 0.1 0 148 1 121 "HapMap,freq,cluster" Borderline 1.041 11 Tolerant 0.44 2.87 24 moderately conservative 223360 9q34 dopamine beta-hydroxylase (dopamine beta-monooxygenase) 122 rs5320 DBH 1621 9 133537027 NM_000787 NP_000778 A/G A197T plus 22886995 1303 SEQUENOM CEPH CEPH (92) 92 0.07 0.04 0.04 210 2 0.1 0 148 1 121 "HapMap,freq,cluster" Borderline 1.041 11 Tolerant 0.44 2.87 24 moderately conservative 223360 9q34 dopamine beta-hydroxylase (dopamine beta-monooxygenase) 123 rs5324 DBH 1621 9 133538212 NM_000787 NP_000778 A/G D276N plus 6786 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.1 0.1 0 120 1 0.06 0.01 126 2 123 "HapMap,submitter,freq,cluster" Borderline 1.029 11 Tolerant 0.22 2.81 27 conservative 223360 9q34 dopamine beta-hydroxylase (dopamine beta-monooxygenase) 124 rs5355 SELE 6401 1 166427528 NM_000450 NP_000441 C/T L575F minus 5111468 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 42 0.05 0.07 0.03 182 3 0.08 0.04 116 2 123 "by cluster,freq" Intolerant 0.04 3.13 23 conservative 131210 1q22-q25 selectin E (endothelial adhesion molecule 1) 125 rs5355 SELE 6401 1 166427528 NM_000450 NP_000441 C/T L575F minus 5111468 1303 SEQUENOM CEPH CEPH (92) 92 0.1 0.07 0.03 182 3 0.08 0.04 116 2 123 "by cluster,freq" Intolerant 0.04 3.13 23 conservative 131210 1q22-q25 selectin E (endothelial adhesion molecule 1) 126 rs5355 SELE 6401 1 166427528 NM_000450 NP_000441 C/T L575F minus 24266318 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.07 0.03 182 3 0.08 0.04 116 2 123 "by cluster,freq" Intolerant 0.04 3.13 23 conservative 131210 1q22-q25 selectin E (endothelial adhesion molecule 1) 127 rs5361 SELE 6401 1 166432718 NM_000450 NP_000441 A/C S149R minus 5111403 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 44 0.09 0.08 0.07 194 3 0.06 0.02 538 6 123 "by cluster,freq" Possibly damaging 1.548 8 Intolerant 0 2.8 52 moderately radical 131210 1q22-q25 selectin E (endothelial adhesion molecule 1) 128 rs5361 SELE 6401 1 166432718 NM_000450 NP_000441 A/C S149R minus 5111403 1303 SEQUENOM CEPH CEPH (92) 92 0.02 0.08 0.07 194 3 0.06 0.02 538 6 123 "by cluster,freq" Possibly damaging 1.548 8 Intolerant 0 2.8 52 moderately radical 131210 1q22-q25 selectin E (endothelial adhesion molecule 1) 129 rs5361 SELE 6401 1 166432718 NM_000450 NP_000441 A/C S149R minus 6903932 775 SNP500CANCER CAUC1 Caucasian (31) 58 0.16 0.08 0.07 194 3 0.06 0.02 538 6 123 "by cluster,freq" Possibly damaging 1.548 8 Intolerant 0 2.8 52 moderately radical 131210 1q22-q25 selectin E (endothelial adhesion molecule 1) 130 rs5368 SELE 6401 1 166428604 NM_000450 NP_000441 C/T H468Y minus 5111428 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 44 0.02 0.03 0.01 184 3 0.18 0.05 1768 5 123 "by submitter,freq,cluster" Probably damaging 2.116 8 moderately conservative 131210 1q22-q25 selectin E (endothelial adhesion molecule 1) 131 rs5368 SELE 6401 1 166428604 NM_000450 NP_000441 C/T H468Y minus 5111428 1303 SEQUENOM CEPH CEPH (92) 92 0.03 0.03 0.01 184 3 0.18 0.05 1768 5 123 "by submitter,freq,cluster" Probably damaging 2.116 8 moderately conservative 131210 1q22-q25 selectin E (endothelial adhesion molecule 1) 132 rs5368 SELE 6401 1 166428604 NM_000450 NP_000441 C/T H468Y minus 23860569 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.03 0.01 184 3 0.18 0.05 1768 5 123 "by submitter,freq,cluster" Probably damaging 2.116 8 moderately conservative 131210 1q22-q25 selectin E (endothelial adhesion molecule 1) 133 rs5370 EDN1 1906 6 12404241 NM_001955 NP_001946 G/T K198N plus 3176606 619 WICVAR MITOGPOP6 CORIELL Mixed 54 0.2 0.28 0.06 812 6 0.27 0.07 1972 6 123 "by doubleHit,freq,cluster" Benign 0.225 10 moderately conservative 131240 6p24.1 endothelin 1 134 rs5370 EDN1 1906 6 12404241 NM_001955 NP_001946 G/T K198N plus 8819730 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.29 0.28 0.06 812 6 0.27 0.07 1972 6 123 "by doubleHit,freq,cluster" Benign 0.225 10 moderately conservative 131240 6p24.1 endothelin 1 135 rs5370 EDN1 1906 6 12404241 NM_001955 NP_001946 G/T K198N plus 14857936 693 EGP_SNPS PDR90 NIHPDR 144 0.23 0.28 0.06 812 6 0.27 0.07 1972 6 123 "by doubleHit,freq,cluster" Benign 0.225 10 moderately conservative 131240 6p24.1 endothelin 1 136 rs5370 EDN1 1906 6 12404241 NM_001955 NP_001946 G/T K198N plus 24787768 1303 SEQUENOM CEPH CEPH (92) 184 0.3 0.28 0.06 812 6 0.27 0.07 1972 6 123 "by doubleHit,freq,cluster" Benign 0.225 10 moderately conservative 131240 6p24.1 endothelin 1 137 rs5370 EDN1 1906 6 12404241 NM_001955 NP_001946 G/T K198N plus 24796004 1303 SEQUENOM CEPH CEPH (92) 184 0.24 0.28 0.06 812 6 0.27 0.07 1972 6 123 "by doubleHit,freq,cluster" Benign 0.225 10 moderately conservative 131240 6p24.1 endothelin 1 138 rs5370 EDN1 1906 6 12404241 NM_001955 NP_001946 G/T K198N plus 24796238 1303 SEQUENOM CEPH CEPH (92) 184 0.36 0.28 0.06 812 6 0.27 0.07 1972 6 123 "by doubleHit,freq,cluster" Benign 0.225 10 moderately conservative 131240 6p24.1 endothelin 1 139 rs5491 ICAM1 3383 19 10246540 NM_000201 NP_000192 A/T K56M plus 5586604 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.02 0.02 0 62 1 0.16 0.14 564 8 123 "HapMap,submitter,freq,cluster" Benign 0.892 12 Potentially intolerant 0.1 2.77 25 moderately conservative 147840 19p13.3-p13.2 "intercellular adhesion molecule 1 (CD54), human rhinovirus receptor" 140 rs5498 ICAM1 3383 19 10256683 NM_000201 NP_000192 A/G K469E plus 3172763 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 62 0.34 0.39 0.06 420 5 0.26 0.1 196 2 123 "by cluster,freq" Potentially damaging 1.464 13 moderately conservative 147840 19p13.3-p13.2 "intercellular adhesion molecule 1 (CD54), human rhinovirus receptor" 141 rs5498 ICAM1 3383 19 10256683 NM_000201 NP_000192 A/G K469E plus 4328201 649 FHCRC POPU1 USA (20) 40 0.33 0.39 0.06 420 5 0.26 0.1 196 2 123 "by cluster,freq" Potentially damaging 1.464 13 moderately conservative 147840 19p13.3-p13.2 "intercellular adhesion molecule 1 (CD54), human rhinovirus receptor" 142 rs5498 ICAM1 3383 19 10256683 NM_000201 NP_000192 A/G K469E plus 7985472 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 42 0.36 0.39 0.06 420 5 0.26 0.1 196 2 123 "by cluster,freq" Potentially damaging 1.464 13 moderately conservative 147840 19p13.3-p13.2 "intercellular adhesion molecule 1 (CD54), human rhinovirus receptor" 143 rs5498 ICAM1 3383 19 10256683 NM_000201 NP_000192 A/G K469E plus 7985472 1303 SEQUENOM CEPH CEPH (92) 92 0.48 0.39 0.06 420 5 0.26 0.1 196 2 123 "by cluster,freq" Potentially damaging 1.464 13 moderately conservative 147840 19p13.3-p13.2 "intercellular adhesion molecule 1 (CD54), human rhinovirus receptor" 144 rs5498 ICAM1 3383 19 10256683 NM_000201 NP_000192 A/G K469E plus 24796638 1303 SEQUENOM CEPH CEPH (92) 184 0.39 0.39 0.06 420 5 0.26 0.1 196 2 123 "by cluster,freq" Potentially damaging 1.464 13 moderately conservative 147840 19p13.3-p13.2 "intercellular adhesion molecule 1 (CD54), human rhinovirus receptor" 145 rs5503 ICAM2 3384 17 59436418 NM_000873 NP_000864 A/G A37T minus 3178070 619 WICVAR MITOGPOP6 CORIELL Mixed 42 0.05 0.05 0 42 1 0.05 0 80 1 102 "by submitter,freq,cluster" Benign 0.909 5 Intolerant 0.04 2.82 26 moderately conservative 146630 17q23-q25 intercellular adhesion molecule 2 146 rs5522 NR3C2 4306 4 149715080 NM_000901 NP_000892 A/G V180I minus 10110564 902 AFFY Caucasian 24 0.08 0.16 0.09 162 3 0.16 0.05 306 6 123 "by submitter,freq,cluster" Benign 0.093 6 conservative 600983 4q31.1 "nuclear receptor subfamily 3, group C, member 2" 147 rs5522 NR3C2 4306 4 149715080 NM_000901 NP_000892 A/G V180I minus 22887609 1303 SEQUENOM CEPH CEPH (92) 92 0.22 0.16 0.09 162 3 0.16 0.05 306 6 123 "by submitter,freq,cluster" Benign 0.093 6 conservative 600983 4q31.1 "nuclear receptor subfamily 3, group C, member 2" 148 rs5522 NR3C2 4306 4 149715080 NM_000901 NP_000892 A/G V180I minus 23731817 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.07 0.16 0.09 162 3 0.16 0.05 306 6 123 "by submitter,freq,cluster" Benign 0.093 6 conservative 600983 4q31.1 "nuclear receptor subfamily 3, group C, member 2" 149 rs5856 NOL5A 10528 20 2586882 NM_006392 NP_006383 C/T V576A plus 8464 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.35 0.35 0 280 2 0.24 0 750 1 121 "by doubleHit,freq,cluster" moderately conservative 20p13 nucleolar protein 5A (56kDa with KKE/D repeat) 150 rs5856 NOL5A 10528 20 2586882 NM_006392 NP_006383 C/T V576A plus 5420265 1303 SEQUENOM CEPH CEPH (92) 92 0.35 0.35 0 280 2 0.24 0 750 1 121 "by doubleHit,freq,cluster" moderately conservative 20p13 nucleolar protein 5A (56kDa with KKE/D repeat) 151 rs5880 CETP 1071 16 55572592 NM_000078 NP_000069 C/G A390P plus 7482 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 114 0.1 0.07 0.04 252 3 0.01 0 328 3 123 "by cluster,freq" Intolerant 0.05 2.82 15 conservative 118470 16q21 "cholesteryl ester transfer protein, plasma" 152 rs5880 CETP 1071 16 55572592 NM_000078 NP_000069 C/G A390P plus 20419188 1303 SEQUENOM CEPH CEPH (92) 92 0.06 0.07 0.04 252 3 0.01 0 328 3 123 "by cluster,freq" Intolerant 0.05 2.82 15 conservative 118470 16q21 "cholesteryl ester transfer protein, plasma" 153 rs5880 CETP 1071 16 55572592 NM_000078 NP_000069 C/G A390P plus 23418077 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.02 0.07 0.04 252 3 0.01 0 328 3 123 "by cluster,freq" Intolerant 0.05 2.82 15 conservative 118470 16q21 "cholesteryl ester transfer protein, plasma" 154 rs5881 CETP 1071 16 55569513 NM_000078 NP_000069 A/G G331S plus 7483 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 114 0.03 0.03 0 114 1 52 HapMap Tolerant 0.73 2.88 14 moderately conservative 118470 16q21 "cholesteryl ester transfer protein, plasma" 155 rs5882 CETP 1071 16 55573593 NM_000078 NP_000069 A/G V422I plus 7484 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 114 0.33 0.32 0.01 162 2 0.43 0.03 378 4 123 "by doubleHit,submitter,freq,cluster" conservative 118470 16q21 "cholesteryl ester transfer protein, plasma" 156 rs5882 CETP 1071 16 55573593 NM_000078 NP_000069 A/G V422I plus 23991710 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.31 0.32 0.01 162 2 0.43 0.03 378 4 123 "by doubleHit,submitter,freq,cluster" conservative 118470 16q21 "cholesteryl ester transfer protein, plasma" 157 rs5887 CETP 1071 16 55575053 NM_000078 NP_000069 A/G V486M plus 7489 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 114 0.03 0.03 0 114 1 123 by freq conservative 118470 16q21 "cholesteryl ester transfer protein, plasma" 158 rs5893 F2R 2149 5 76064302 NM_001992 NP_001983 A/G S166G plus 7495 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 106 0.03 0.03 0 106 1 52 by freq Borderline 1.142 8 Potentially intolerant 0.07 2.79 25 moderately conservative 187930 5q13 coagulation factor II (thrombin) receptor 159 rs5896 F2 2147 11 46701579 NM_000506 NP_000497 C/T T165M plus 7498 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 126 0.1 0.11 0.08 432 5 0.16 0.23 138 3 123 "HapMap,submitter,freq,cluster" Possibly damaging 1.602 10 Potentially intolerant 0.1 2.9 26 moderately conservative 176930 11p11-q12 coagulation factor II (thrombin) 160 rs5896 F2 2147 11 46701579 NM_000506 NP_000497 C/T T165M plus 4384736 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.07 0.11 0.08 432 5 0.16 0.23 138 3 123 "HapMap,submitter,freq,cluster" Possibly damaging 1.602 10 Potentially intolerant 0.1 2.9 26 moderately conservative 176930 11p11-q12 coagulation factor II (thrombin) 161 rs5896 F2 2147 11 46701579 NM_000506 NP_000497 C/T T165M plus 4384736 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.05 0.11 0.08 432 5 0.16 0.23 138 3 123 "HapMap,submitter,freq,cluster" Possibly damaging 1.602 10 Potentially intolerant 0.1 2.9 26 moderately conservative 176930 11p11-q12 coagulation factor II (thrombin) 162 rs5896 F2 2147 11 46701579 NM_000506 NP_000497 C/T T165M plus 4384736 1303 SEQUENOM CEPH CEPH (92) 92 0.24 0.11 0.08 432 5 0.16 0.23 138 3 123 "HapMap,submitter,freq,cluster" Possibly damaging 1.602 10 Potentially intolerant 0.1 2.9 26 moderately conservative 176930 11p11-q12 coagulation factor II (thrombin) 163 rs5896 F2 2147 11 46701579 NM_000506 NP_000497 C/T T165M plus 24181221 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.11 0.08 432 5 0.16 0.23 138 3 123 "HapMap,submitter,freq,cluster" Possibly damaging 1.602 10 Potentially intolerant 0.1 2.9 26 moderately conservative 176930 11p11-q12 coagulation factor II (thrombin) 164 rs5897 F2 2147 11 46706147 NM_000506 NP_000497 A/C P386T plus 7499 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 128 0.03 0.03 0 128 1 52 HapMap Probably damaging 2.396 10 Tolerant 0.41 2.8 35 conservative 176930 11p11-q12 coagulation factor II (thrombin) 165 rs5901 F3 2152 1 94710771 NM_001993 NP_001984 C/T R163W minus 7503 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 86 0.03 0.03 0 86 1 121 "by cluster,freq" Benign 0.737 19 Borderline 0.11 2.87 16 moderately radical 134390 1p22-p21 "coagulation factor III (thromboplastin, tissue factor)" 166 rs5911 ITGA2B 3674 17 39808591 NM_000419 NP_000410 A/C I874S plus 7514 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 112 0.1 0.2 0.14 230 2 0.43 0 1498 1 121 "HapMap,doubleHit,freq,cluster" Benign 0.003 13 Tolerant 0.45 2.82 20 moderately radical 607759 17q21.32 "integrin, alpha 2b (platelet glycoprotein IIb of IIb/IIIa complex, antigen CD41B)" 167 rs5911 ITGA2B 3674 17 39808591 NM_000419 NP_000410 A/C I874S plus 2394254 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.3 0.2 0.14 230 2 0.43 0 1498 1 121 "HapMap,doubleHit,freq,cluster" Benign 0.003 13 Tolerant 0.45 2.82 20 moderately radical 607759 17q21.32 "integrin, alpha 2b (platelet glycoprotein IIb of IIb/IIIa complex, antigen CD41B)" 168 rs5914 ITGA2B 3674 17 39807594 NM_000419 NP_000410 A/T Y968N minus 7517 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 112 0.03 0.03 0 112 1 52 by freq Probably damaging 2.407 11 Intolerant 0.01 2.77 23 moderately radical 607759 17q21.32 "integrin, alpha 2b (platelet glycoprotein IIb of IIb/IIIa complex, antigen CD41B)" 169 rs5915 ITGA2B 3674 17 39822249 NM_000419 NP_000410 C/T T40I minus 7518 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 112 0.03 0.03 0 112 1 52 HapMap Possibly damaging 1.749 8 Intolerant 0.01 2.76 22 moderately conservative 607759 17q21.32 "integrin, alpha 2b (platelet glycoprotein IIb of IIb/IIIa complex, antigen CD41B)" 170 rs5917 ITGB3 3690 17 42716952 NM_000212 NP_000203 A/G R169Q plus 7520 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 106 0.03 0.03 0 106 1 121 "by cluster,freq" Possibly damaging 1.527 28 Borderline 0.12 2.87 51 conservative 173470 17q21.32 "integrin, beta 3 (platelet glycoprotein IIIa, antigen CD61)" 171 rs5918 ITGB3 3690 17 42715729 NM_000212 NP_000203 C/T L59P plus 7521 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 98 0.1 0.1 0 98 1 52 by freq Benign 0.984 18 Tolerant 0.31 2.95 44 moderately conservative 173470 17q21.32 "integrin, beta 3 (platelet glycoprotein IIIa, antigen CD61)" 172 rs5921 ITGB3 3690 17 42724600 NM_000212 NP_000203 A/G V453I plus 7526 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 106 0.03 0.03 0 106 1 52 by freq Benign 0.031 28 Tolerant 0.56 2.87 52 conservative 173470 17q21.32 "integrin, beta 3 (platelet glycoprotein IIIa, antigen CD61)" 173 rs5928 LDLR 3949 19 11101240 NM_000527 NP_000518 A/G R814Q plus 7533 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 126 0.03 0.03 0 126 1 52 by freq Benign 0.115 34 Tolerant 0.81 2.94 40 conservative 606945 19p13.3 low density lipoprotein receptor (familial hypercholesterolemia) 174 rs5931 LDLR 3949 19 11061228 NM_000527 NP_000518 C/G G2R plus 7537 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 126 0.03 0.03 0 126 1 52 HapMap moderately radical 606945 19p13.3 low density lipoprotein receptor (familial hypercholesterolemia) 175 rs5938 PTAFR 5724 1 28161004 NM_000952 NP_000943 A/C A224D minus 7545 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 114 0.03 0.03 0 114 1 0.1 0 1548 2 123 "by cluster,freq" Potentially damaging 1.329 11 Potentially intolerant 0.08 2.78 33 moderately radical 173393 1p35-p34.3 platelet-activating factor receptor 176 rs5939 PTAFR 5724 1 28160662 NM_000952 NP_000943 A/G N338S minus 7546 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 114 0.03 0.03 0 114 1 0.09 0 46 1 123 "by submitter,freq,cluster" Borderline 1.242 7 conservative 173393 1p35-p34.3 platelet-activating factor receptor 177 rs5954 APOD 347 3 529568 NM_001647 NP_001638 C/T S115L minus 7564 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 108 0.03 0.03 0 108 1 52 by freq Possibly damaging 1.675 8 Tolerant 0.46 2.76 16 moderately radical 107740 3q26.2-qter apolipoprotein D 178 rs5961 F10 2159 13 112831786 NM_000504 NP_000495 C/G Q30H plus 7571 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 108 0.03 0.02 0.01 200 2 0.04 0 46 1 123 "by cluster,freq" Borderline 1.24 10 Borderline 0.12 2.8 24 conservative 227600 13q34 coagulation factor X 179 rs5961 F10 2159 13 112831786 NM_000504 NP_000495 C/G Q30H plus 7571 1303 SEQUENOM CEPH CEPH (92) 92 0.01 0.02 0.01 200 2 0.04 0 46 1 123 "by cluster,freq" Borderline 1.24 10 Borderline 0.12 2.8 24 conservative 227600 13q34 coagulation factor X 180 rs5963 F10 2159 13 112825189 NM_000504 NP_000495 A/C L7I plus 7573 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 108 0.03 0.03 0 108 1 52 by freq Intolerant 0.05 3.09 11 conservative 227600 13q34 coagulation factor X 181 rs5968 F11 2160 4 187568053 NM_000128 NP_000119 C/T P66L plus 7578 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 108 0.03 0.03 0 108 1 52 by freq Possibly damaging 1.74 10 moderately conservative 264900 4q35 coagulation factor XI (plasma thromboplastin antecedent) 182 rs5969 F11 2160 4 187572669 NM_000128 NP_000119 A/G Q244R plus 7579 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 104 0.03 0.03 0 104 1 52 by freq Potentially damaging 1.359 14 conservative 264900 4q35 coagulation factor XI (plasma thromboplastin antecedent) 183 rs5972 F11 2160 4 187576582 NM_000128 NP_000119 A/T I308F plus 7582 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 108 0.03 0.03 0 108 1 52 by freq Possibly damaging 1.564 14 Intolerant 0.01 2.87 54 conservative 264900 4q35 coagulation factor XI (plasma thromboplastin antecedent) 184 rs5982 F13A1 2162 6 6119865 NM_000129 NP_000120 C/T P565L minus 7592 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 106 0.1 0.18 0.11 198 3 0.13 0.04 132 3 123 "by doubleHit,freq,cluster" Potentially intolerant 0.1 2.78 18 moderately conservative 134570 6p25.3-p24.3 "coagulation factor XIII, A1 polypeptide" 185 rs5982 F13A1 2162 6 6119865 NM_000129 NP_000120 C/T P565L minus 4250318 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 44 0.27 0.18 0.11 198 3 0.13 0.04 132 3 123 "by doubleHit,freq,cluster" Potentially intolerant 0.1 2.78 18 moderately conservative 134570 6p25.3-p24.3 "coagulation factor XIII, A1 polypeptide" 186 rs5982 F13A1 2162 6 6119865 NM_000129 NP_000120 C/T P565L minus 24334604 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.29 0.18 0.11 198 3 0.13 0.04 132 3 123 "by doubleHit,freq,cluster" Potentially intolerant 0.1 2.78 18 moderately conservative 134570 6p25.3-p24.3 "coagulation factor XIII, A1 polypeptide" 187 rs5983 F13A1 2162 6 6112832 NM_000129 NP_000120 A/T L589Q minus 7593 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 106 0.03 0.03 0 106 1 52 by freq Tolerant 0.56 2.78 18 moderately radical 134570 6p25.3-p24.3 "coagulation factor XIII, A1 polypeptide" 188 rs5984 F13A1 2162 6 6119907 NM_000129 NP_000120 C/T T551I minus 7594 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 108 0.03 0.03 0 108 1 123 by freq Tolerant 0.34 2.78 18 moderately conservative 134570 6p25.3-p24.3 "coagulation factor XIII, A1 polypeptide" 189 rs5985 F13A1 2162 6 6263794 NM_000129 NP_000120 G/T V35L minus 7595 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 108 0.03 0.2 0.2 242 3 0.2 0 44 1 120 "by doubleHit,freq,cluster" Tolerant 0.49 2.92 14 conservative 134570 6p25.3-p24.3 "coagulation factor XIII, A1 polypeptide" 190 rs5985 F13A1 2162 6 6263794 NM_000129 NP_000120 G/T V35L minus 4250177 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 42 0.24 0.2 0.2 242 3 0.2 0 44 1 120 "by doubleHit,freq,cluster" Tolerant 0.49 2.92 14 conservative 134570 6p25.3-p24.3 "coagulation factor XIII, A1 polypeptide" 191 rs5985 F13A1 2162 6 6263794 NM_000129 NP_000120 G/T V35L minus 19693415 1303 SEQUENOM CEPH CEPH (92) 92 0.39 0.2 0.2 242 3 0.2 0 44 1 120 "by doubleHit,freq,cluster" Tolerant 0.49 2.92 14 conservative 134570 6p25.3-p24.3 "coagulation factor XIII, A1 polypeptide" 192 rs5987 F13A1 2162 6 6097139 NM_000129 NP_000120 A/G V651I minus 7597 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 108 0.1 0.11 0.01 246 3 0.04 0 46 1 121 "by cluster,freq" Tolerant 1 2.78 18 conservative 134570 6p25.3-p24.3 "coagulation factor XIII, A1 polypeptide" 193 rs5987 F13A1 2162 6 6097139 NM_000129 NP_000120 A/G V651I minus 4250337 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.09 0.11 0.01 246 3 0.04 0 46 1 121 "by cluster,freq" Tolerant 1 2.78 18 conservative 134570 6p25.3-p24.3 "coagulation factor XIII, A1 polypeptide" 194 rs5987 F13A1 2162 6 6097139 NM_000129 NP_000120 A/G V651I minus 4250337 1303 SEQUENOM CEPH CEPH (92) 92 0.12 0.11 0.01 246 3 0.04 0 46 1 121 "by cluster,freq" Tolerant 1 2.78 18 conservative 134570 6p25.3-p24.3 "coagulation factor XIII, A1 polypeptide" 195 rs5988 F13A1 2162 6 6097136 NM_000129 NP_000120 C/G E652Q minus 7598 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 106 0.33 0.27 0.07 244 3 0.17 0 46 1 123 "by cluster,freq" conservative 134570 6p25.3-p24.3 "coagulation factor XIII, A1 polypeptide" 196 rs5988 F13A1 2162 6 6097136 NM_000129 NP_000120 C/G E652Q minus 4250338 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.28 0.27 0.07 244 3 0.17 0 46 1 123 "by cluster,freq" conservative 134570 6p25.3-p24.3 "coagulation factor XIII, A1 polypeptide" 197 rs5988 F13A1 2162 6 6097136 NM_000129 NP_000120 C/G E652Q minus 4250338 1303 SEQUENOM CEPH CEPH (92) 92 0.2 0.27 0.07 244 3 0.17 0 46 1 123 "by cluster,freq" conservative 134570 6p25.3-p24.3 "coagulation factor XIII, A1 polypeptide" 198 rs6065 GP1BA 2811 17 4777161 NM_000173 NP_000164 C/T T161M plus 3199559 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.02 0.04 0.02 138 2 0.17 0 48 1 121 "by cluster,freq" Potentially damaging 1.35 8 Borderline 0.11 2.86 260 moderately conservative 606672 17pter-p12 "glycoprotein Ib (platelet), alpha polypeptide" 199 rs6065 GP1BA 2811 17 4777161 NM_000173 NP_000164 C/T T161M plus 3199559 1303 SEQUENOM CEPH CEPH (92) 92 0.05 0.04 0.02 138 2 0.17 0 48 1 121 "by cluster,freq" Potentially damaging 1.35 8 Borderline 0.11 2.86 260 moderately conservative 606672 17pter-p12 "glycoprotein Ib (platelet), alpha polypeptide" 200 rs6068 GP1BA 2811 17 4776894 NM_000173 NP_000164 A/G R72H plus 7685 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 98 0.03 0.03 0 98 1 52 by freq Borderline 1.125 8 Tolerant 1 2.79 246 conservative 606672 17pter-p12 "glycoprotein Ib (platelet), alpha polypeptide" 201 rs6078 LIPC 3990 15 56621285 NM_000236 NP_000227 A/G V95M plus 7695 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 102 0.1 0.06 0.04 266 3 0.15 0.18 94 2 123 "HapMap,freq" Potentially damaging 1.334 8 Tolerant 0.76 2.8 41 conservative 151670 15q21-q23 "lipase, hepatic" 202 rs6078 LIPC 3990 15 56621285 NM_000236 NP_000227 A/G V95M plus 7695 885 TSC-CSHL HapMap-CEPH-30-trios 116 0.03 0.06 0.04 266 3 0.15 0.18 94 2 123 "HapMap,freq" Potentially damaging 1.334 8 Tolerant 0.76 2.8 41 conservative 151670 15q21-q23 "lipase, hepatic" 203 rs6078 LIPC 3990 15 56621285 NM_000236 NP_000227 A/G V95M plus 24224736 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.06 0.04 266 3 0.15 0.18 94 2 123 "HapMap,freq" Potentially damaging 1.334 8 Tolerant 0.76 2.8 41 conservative 151670 15q21-q23 "lipase, hepatic" 204 rs6079 LIPC 3990 15 56643145 NM_000236 NP_000227 A/G S440N plus 7696 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 106 0.03 0.03 0 106 1 52 HapMap Benign 0 8 Tolerant 0.6 2.97 39 conservative 151670 15q21-q23 "lipase, hepatic" 205 rs6083 LIPC 3990 15 56625302 NM_000236 NP_000227 A/G N215S plus 7700 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 104 0.33 0.38 0.02 1283 5 0.29 0.11 94 2 123 "HapMap,doubleHit,freq,cluster" Potentially damaging 1.386 8 Potentially intolerant 0.06 2.8 45 conservative 151670 15q21-q23 "lipase, hepatic" 206 rs6083 LIPC 3990 15 56625302 NM_000236 NP_000227 A/G N215S plus 6587908 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.42 0.38 0.02 1283 5 0.29 0.11 94 2 123 "HapMap,doubleHit,freq,cluster" Potentially damaging 1.386 8 Potentially intolerant 0.06 2.8 45 conservative 151670 15q21-q23 "lipase, hepatic" 207 rs6083 LIPC 3990 15 56625302 NM_000236 NP_000227 A/G N215S plus 6587908 1303 SEQUENOM CEPH CEPH (92) 92 0.36 0.38 0.02 1283 5 0.29 0.11 94 2 123 "HapMap,doubleHit,freq,cluster" Potentially damaging 1.386 8 Potentially intolerant 0.06 2.8 45 conservative 151670 15q21-q23 "lipase, hepatic" 208 rs6083 LIPC 3990 15 56625302 NM_000236 NP_000227 A/G N215S plus 12587368 928 IBARROSO ELY UK (Ely region of East Anglia) 921 0.38 0.38 0.02 1283 5 0.29 0.11 94 2 123 "HapMap,doubleHit,freq,cluster" Potentially damaging 1.386 8 Potentially intolerant 0.06 2.8 45 conservative 151670 15q21-q23 "lipase, hepatic" 209 rs6083 LIPC 3990 15 56625302 NM_000236 NP_000227 A/G N215S plus 24718495 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.41 0.38 0.02 1283 5 0.29 0.11 94 2 123 "HapMap,doubleHit,freq,cluster" Potentially damaging 1.386 8 Potentially intolerant 0.06 2.8 45 conservative 151670 15q21-q23 "lipase, hepatic" 210 rs6087 MPL 4352 1 43472956 NM_005373 NP_005364 C/T A58V plus 7704 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 104 0.03 0.03 0 104 1 52 by freq Borderline 1.227 7 Tolerant 0.32 2.8 19 moderately conservative 159530 1p34 myeloproliferative leukemia virus oncogene 211 rs6088 MPL 4352 1 43474145 NM_005373 NP_005364 A/G E168K plus 7705 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 102 0.03 0.03 0 102 1 52 by freq Potentially damaging 1.267 6 Potentially intolerant 0.08 2.87 19 moderately conservative 159530 1p34 myeloproliferative leukemia virus oncogene 212 rs6090 SERPINE1 5054 7 100365158 NM_000602 NP_000593 A/G V17I plus 7707 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 106 0.03 0.03 0.01 154 2 0.12 0.06 225 4 123 "by submitter,freq,cluster" Benign 0.106 6 Borderline 0.19 3.23 11 conservative 173360 7q21.3-q22 "serine (or cysteine) proteinase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1" 213 rs6090 SERPINE1 5054 7 100365158 NM_000602 NP_000593 A/G V17I plus 23411103 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.03 0.01 154 2 0.12 0.06 225 4 123 "by submitter,freq,cluster" Benign 0.106 6 Borderline 0.19 3.23 11 conservative 173360 7q21.3-q22 "serine (or cysteine) proteinase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1" 214 rs6092 SERPINE1 5054 7 100365152 NM_000602 NP_000593 A/G A15T plus 7709 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 106 0.1 0.12 0.04 250 4 0.13 0.01 125 2 123 "by cluster,freq" Benign 0.937 6 Potentially intolerant 0.08 3.23 11 moderately conservative 173360 7q21.3-q22 "serine (or cysteine) proteinase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1" 215 rs6092 SERPINE1 5054 7 100365152 NM_000602 NP_000593 A/G A15T plus 3172290 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 4 0.25 0.12 0.04 250 4 0.13 0.01 125 2 123 "by cluster,freq" Benign 0.937 6 Potentially intolerant 0.08 3.23 11 moderately conservative 173360 7q21.3-q22 "serine (or cysteine) proteinase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1" 216 rs6092 SERPINE1 5054 7 100365152 NM_000602 NP_000593 A/G A15T plus 3172290 1303 SEQUENOM CEPH CEPH (92) 92 0.16 0.12 0.04 250 4 0.13 0.01 125 2 123 "by cluster,freq" Benign 0.937 6 Potentially intolerant 0.08 3.23 11 moderately conservative 173360 7q21.3-q22 "serine (or cysteine) proteinase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1" 217 rs6092 SERPINE1 5054 7 100365152 NM_000602 NP_000593 A/G A15T plus 23987545 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.12 0.04 250 4 0.13 0.01 125 2 123 "by cluster,freq" Benign 0.937 6 Potentially intolerant 0.08 3.23 11 moderately conservative 173360 7q21.3-q22 "serine (or cysteine) proteinase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1" 218 rs6098 SERPINB2 5055 18 59715374 NM_002575 NP_002566 A/G N120D plus 7715 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 104 0.33 0.24 0.07 364 4 0.41 0.09 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 0.97 2.83 59 conservative 173390 18q21.3 "serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 2" 219 rs6098 SERPINB2 5055 18 59715374 NM_002575 NP_002566 A/G N120D plus 3094604 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.23 0.24 0.07 364 4 0.41 0.09 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 0.97 2.83 59 conservative 173390 18q21.3 "serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 2" 220 rs6098 SERPINB2 5055 18 59715374 NM_002575 NP_002566 A/G N120D plus 3094604 1303 SEQUENOM CEPH CEPH (92) 92 0.16 0.24 0.07 364 4 0.41 0.09 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 0.97 2.83 59 conservative 173390 18q21.3 "serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 2" 221 rs6098 SERPINB2 5055 18 59715374 NM_002575 NP_002566 A/G N120D plus 23531315 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.24 0.07 364 4 0.41 0.09 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 0.97 2.83 59 conservative 173390 18q21.3 "serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 2" 222 rs6100 SERPINB2 5055 18 59720625 NM_002575 NP_002566 A/G R229H plus 7717 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 96 0.03 0.03 0 96 1 52 HapMap Potentially intolerant 0.06 2.83 59 conservative 173390 18q21.3 "serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 2" 223 rs6103 SERPINB2 5055 18 59721483 NM_002575 NP_002566 C/G N404K plus 7720 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 106 0.33 0.25 0.06 310 5 0.38 0.08 166 5 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 0.31 2.83 59 moderately conservative 173390 18q21.3 "serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 2" 224 rs6103 SERPINB2 5055 18 59721483 NM_002575 NP_002566 C/G N404K plus 7720 902 AFFY Caucasian 24 0.17 0.25 0.06 310 5 0.38 0.08 166 5 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 0.31 2.83 59 moderately conservative 173390 18q21.3 "serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 2" 225 rs6103 SERPINB2 5055 18 59721483 NM_002575 NP_002566 C/G N404K plus 7720 904 AFFY CEPH 12 0.17 0.25 0.06 310 5 0.38 0.08 166 5 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 0.31 2.83 59 moderately conservative 173390 18q21.3 "serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 2" 226 rs6103 SERPINB2 5055 18 59721483 NM_002575 NP_002566 C/G N404K plus 14303771 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.23 0.25 0.06 310 5 0.38 0.08 166 5 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 0.31 2.83 59 moderately conservative 173390 18q21.3 "serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 2" 227 rs6103 SERPINB2 5055 18 59721483 NM_002575 NP_002566 C/G N404K plus 23531504 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.25 0.06 310 5 0.38 0.08 166 5 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 0.31 2.83 59 moderately conservative 173390 18q21.3 "serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 2" 228 rs6104 SERPINB2 5055 18 59721509 NM_002575 NP_002566 C/G S413C plus 7721 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 106 0.33 0.29 0.08 154 2 0.41 0.09 94 2 123 "by doubleHit,submitter,freq,cluster" Tolerant 0.29 2.83 59 moderately radical 173390 18q21.3 "serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 2" 229 rs6104 SERPINB2 5055 18 59721509 NM_002575 NP_002566 C/G S413C plus 23531513 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.29 0.08 154 2 0.41 0.09 94 2 123 "by doubleHit,submitter,freq,cluster" Tolerant 0.29 2.83 59 moderately radical 173390 18q21.3 "serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 2" 230 rs6114 SERPINA5 5104 14 94126160 NM_000624 NP_000615 C/G G217R plus 7731 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 106 0.03 0.03 0 106 1 0.07 0 92 2 123 "by submitter,freq,cluster" Potentially damaging 1.273 8 Tolerant 0.3 2.76 79 moderately radical 601841 14q32.1 "serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 5" 231 rs6115 SERPINA5 5104 14 94123643 NM_000624 NP_000615 A/G S64N plus 7732 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 102 0.1 0.2 0.12 240 3 0.11 0 46 1 120 "by doubleHit,freq,cluster" Potentially damaging 1.494 7 conservative 601841 14q32.1 "serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 5" 232 rs6115 SERPINA5 5104 14 94123643 NM_000624 NP_000615 A/G S64N plus 1382288 1303 SEQUENOM CEPH CEPH (92) 92 0.23 0.2 0.12 240 3 0.11 0 46 1 120 "by doubleHit,freq,cluster" Potentially damaging 1.494 7 conservative 601841 14q32.1 "serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 5" 233 rs6115 SERPINA5 5104 14 94123643 NM_000624 NP_000615 A/G S64N plus 2982120 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.37 0.2 0.12 240 3 0.11 0 46 1 120 "by doubleHit,freq,cluster" Potentially damaging 1.494 7 conservative 601841 14q32.1 "serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 5" 234 rs6118 SERPINA5 5104 14 94123616 NM_000624 NP_000615 C/T A55V plus 7735 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 102 0.1 0.08 0.03 288 4 0.33 0.14 140 3 123 "by cluster,freq" Borderline 1.227 7 Tolerant 0.31 2.75 77 moderately conservative 601841 14q32.1 "serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 5" 235 rs6118 SERPINA5 5104 14 94123616 NM_000624 NP_000615 C/T A55V plus 1372189 1303 SEQUENOM CEPH CEPH (92) 92 0.04 0.08 0.03 288 4 0.33 0.14 140 3 123 "by cluster,freq" Borderline 1.227 7 Tolerant 0.31 2.75 77 moderately conservative 601841 14q32.1 "serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 5" 236 rs6118 SERPINA5 5104 14 94123616 NM_000624 NP_000615 C/T A55V plus 2982119 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.09 0.08 0.03 288 4 0.33 0.14 140 3 123 "by cluster,freq" Borderline 1.227 7 Tolerant 0.31 2.75 77 moderately conservative 601841 14q32.1 "serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 5" 237 rs6118 SERPINA5 5104 14 94123616 NM_000624 NP_000615 C/T A55V plus 23648710 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.08 0.03 288 4 0.33 0.14 140 3 123 "by cluster,freq" Borderline 1.227 7 Tolerant 0.31 2.75 77 moderately conservative 601841 14q32.1 "serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 5" 238 rs6119 SERPINA5 5104 14 94123765 NM_000624 NP_000615 A/G K105E plus 7736 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 102 0.03 0.12 0.11 284 4 0.33 0.16 132 3 123 "by doubleHit,freq,cluster" Benign 0.075 7 Tolerant 0.38 2.76 79 moderately conservative 601841 14q32.1 "serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 5" 239 rs6119 SERPINA5 5104 14 94123765 NM_000624 NP_000615 A/G K105E plus 2982123 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 44 0.09 0.12 0.11 284 4 0.33 0.16 132 3 123 "by doubleHit,freq,cluster" Benign 0.075 7 Tolerant 0.38 2.76 79 moderately conservative 601841 14q32.1 "serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 5" 240 rs6119 SERPINA5 5104 14 94123765 NM_000624 NP_000615 A/G K105E plus 12279178 1303 SEQUENOM CEPH CEPH (92) 92 0.26 0.12 0.11 284 4 0.33 0.16 132 3 123 "by doubleHit,freq,cluster" Benign 0.075 7 Tolerant 0.38 2.76 79 moderately conservative 601841 14q32.1 "serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 5" 241 rs6119 SERPINA5 5104 14 94123765 NM_000624 NP_000615 A/G K105E plus 23648718 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.09 0.12 0.11 284 4 0.33 0.16 132 3 123 "by doubleHit,freq,cluster" Benign 0.075 7 Tolerant 0.38 2.76 79 moderately conservative 601841 14q32.1 "serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 5" 242 rs6120 SERPINA5 5104 14 94123813 NM_000624 NP_000615 C/G P121A plus 7737 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 102 0.03 0.03 0 102 1 52 by freq Probably damaging 2.1 7 Intolerant 0.01 2.76 79 conservative 601841 14q32.1 "serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 5" 243 rs6125 SELP 6403 1 166313975 NM_003005 NP_002996 A/G V209M minus 5111836 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.02 0.02 0 46 1 0.05 0 42 1 108 "by cluster,freq" Intolerant 0.04 2.84 42 conservative 173610 1q22-q25 "selectin P (granule membrane protein 140kDa, antigen CD62)" 244 rs6127 SELP 6403 1 166297971 NM_003005 NP_002996 A/G D603N minus 7744 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 102 0.33 0.34 0.1 698 5 0.24 0 46 1 123 "by doubleHit,freq,cluster" Potentially damaging 1.494 5 conservative 173610 1q22-q25 "selectin P (granule membrane protein 140kDa, antigen CD62)" 245 rs6127 SELP 6403 1 166297971 NM_003005 NP_002996 A/G D603N minus 5111936 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 44 0.45 0.34 0.1 698 5 0.24 0 46 1 123 "by doubleHit,freq,cluster" Potentially damaging 1.494 5 conservative 173610 1q22-q25 "selectin P (granule membrane protein 140kDa, antigen CD62)" 246 rs6127 SELP 6403 1 166297971 NM_003005 NP_002996 A/G D603N minus 24796122 1303 SEQUENOM CEPH CEPH (92) 184 0.31 0.34 0.1 698 5 0.24 0 46 1 123 "by doubleHit,freq,cluster" Potentially damaging 1.494 5 conservative 173610 1q22-q25 "selectin P (granule membrane protein 140kDa, antigen CD62)" 247 rs6127 SELP 6403 1 166297971 NM_003005 NP_002996 A/G D603N minus 24811825 1303 SEQUENOM CEPH CEPH (92) 184 0.47 0.34 0.1 698 5 0.24 0 46 1 123 "by doubleHit,freq,cluster" Potentially damaging 1.494 5 conservative 173610 1q22-q25 "selectin P (granule membrane protein 140kDa, antigen CD62)" 248 rs6127 SELP 6403 1 166297971 NM_003005 NP_002996 A/G D603N minus 24811973 1303 SEQUENOM CEPH CEPH (92) 184 0.23 0.34 0.1 698 5 0.24 0 46 1 123 "by doubleHit,freq,cluster" Potentially damaging 1.494 5 conservative 173610 1q22-q25 "selectin P (granule membrane protein 140kDa, antigen CD62)" 249 rs6130 SELP 6403 1 166307865 NM_003005 NP_002996 C/T S500F minus 7747 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 106 0.03 0.03 0 106 1 52 by freq Benign 0.675 5 Borderline 0.11 2.93 37 radical 173610 1q22-q25 "selectin P (granule membrane protein 140kDa, antigen CD62)" 250 rs6131 SELP 6403 1 166312543 NM_003005 NP_002996 A/G S331N minus 7748 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 106 0.1 0.13 0.03 292 4 0.23 0.03 142 3 123 "by doubleHit,freq,cluster" Benign 0.126 5 Tolerant 0.48 3.14 35 conservative 173610 1q22-q25 "selectin P (granule membrane protein 140kDa, antigen CD62)" 251 rs6131 SELP 6403 1 166312543 NM_003005 NP_002996 A/G S331N minus 5111846 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.13 0.13 0.03 292 4 0.23 0.03 142 3 123 "by doubleHit,freq,cluster" Benign 0.126 5 Tolerant 0.48 3.14 35 conservative 173610 1q22-q25 "selectin P (granule membrane protein 140kDa, antigen CD62)" 252 rs6131 SELP 6403 1 166312543 NM_003005 NP_002996 A/G S331N minus 5111846 1303 SEQUENOM CEPH CEPH (92) 92 0.16 0.13 0.03 292 4 0.23 0.03 142 3 123 "by doubleHit,freq,cluster" Benign 0.126 5 Tolerant 0.48 3.14 35 conservative 173610 1q22-q25 "selectin P (granule membrane protein 140kDa, antigen CD62)" 253 rs6131 SELP 6403 1 166312543 NM_003005 NP_002996 A/G S331N minus 23188337 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.13 0.03 292 4 0.23 0.03 142 3 123 "by doubleHit,freq,cluster" Benign 0.126 5 Tolerant 0.48 3.14 35 conservative 173610 1q22-q25 "selectin P (granule membrane protein 140kDa, antigen CD62)" 254 rs6133 SELP 6403 1 166297004 NM_003005 NP_002996 G/T V640L minus 7750 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 104 0.33 0.16 0.15 290 4 0.46 0 94 2 123 "by doubleHit,freq,cluster" Benign 0.31 5 conservative 173610 1q22-q25 "selectin P (granule membrane protein 140kDa, antigen CD62)" 255 rs6133 SELP 6403 1 166297004 NM_003005 NP_002996 G/T V640L minus 5111948 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.04 0.16 0.15 290 4 0.46 0 94 2 123 "by doubleHit,freq,cluster" Benign 0.31 5 conservative 173610 1q22-q25 "selectin P (granule membrane protein 140kDa, antigen CD62)" 256 rs6133 SELP 6403 1 166297004 NM_003005 NP_002996 G/T V640L minus 5111948 1303 SEQUENOM CEPH CEPH (92) 92 0.09 0.16 0.15 290 4 0.46 0 94 2 123 "by doubleHit,freq,cluster" Benign 0.31 5 conservative 173610 1q22-q25 "selectin P (granule membrane protein 140kDa, antigen CD62)" 257 rs6133 SELP 6403 1 166297004 NM_003005 NP_002996 G/T V640L minus 23161353 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.16 0.15 290 4 0.46 0 94 2 123 "by doubleHit,freq,cluster" Benign 0.31 5 conservative 173610 1q22-q25 "selectin P (granule membrane protein 140kDa, antigen CD62)" 258 rs6134 SELP 6403 1 166312442 NM_003005 NP_002996 A/G M365V minus 7751 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 106 0.03 0.03 0 106 1 52 by freq Benign 0.98 5 Tolerant 1 3.14 35 conservative 173610 1q22-q25 "selectin P (granule membrane protein 140kDa, antigen CD62)" 259 rs6136 SELP 6403 1 166295609 NM_003005 NP_002996 A/C T756P minus 7753 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 106 0.1 0.1 0.03 290 4 0.02 0 90 2 123 "by submitter,freq,cluster" Potentially damaging 1.357 5 Borderline 0.15 3.11 24 conservative 173610 1q22-q25 "selectin P (granule membrane protein 140kDa, antigen CD62)" 260 rs6136 SELP 6403 1 166295609 NM_003005 NP_002996 A/C T756P minus 5111969 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 44 0.14 0.1 0.03 290 4 0.02 0 90 2 123 "by submitter,freq,cluster" Potentially damaging 1.357 5 Borderline 0.15 3.11 24 conservative 173610 1q22-q25 "selectin P (granule membrane protein 140kDa, antigen CD62)" 261 rs6136 SELP 6403 1 166295609 NM_003005 NP_002996 A/C T756P minus 5111969 1303 SEQUENOM CEPH CEPH (92) 92 0.06 0.1 0.03 290 4 0.02 0 90 2 123 "by submitter,freq,cluster" Potentially damaging 1.357 5 Borderline 0.15 3.11 24 conservative 173610 1q22-q25 "selectin P (granule membrane protein 140kDa, antigen CD62)" 262 rs6136 SELP 6403 1 166295609 NM_003005 NP_002996 A/C T756P minus 24265196 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.1 0.03 290 4 0.02 0 90 2 123 "by submitter,freq,cluster" Potentially damaging 1.357 5 Borderline 0.15 3.11 24 conservative 173610 1q22-q25 "selectin P (granule membrane protein 140kDa, antigen CD62)" 263 rs6149 VLDLR 7436 9 2625545 NM_003383 NP_003374 A/G V59I plus 7770 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 106 0.03 0.02 0.01 226 2 0.22 0 46 1 123 "HapMap,freq,cluster" Benign 0.143 9 Tolerant 0.22 2.91 37 conservative 192977 9p24 very low density lipoprotein receptor 264 rs6149 VLDLR 7436 9 2625545 NM_003383 NP_003374 A/G V59I plus 7770 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.01 0.02 0.01 226 2 0.22 0 46 1 123 "HapMap,freq,cluster" Benign 0.143 9 Tolerant 0.22 2.91 37 conservative 192977 9p24 very low density lipoprotein receptor 265 rs6180 GHR 2690 5 42754996 NM_000163 NP_000154 A/C I544L plus 7802 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 86 0.33 0.43 0.06 392 6 0.43 0.03 480 8 123 "by doubleHit,freq,cluster" Potentially damaging 1.362 25 Borderline 0.15 2.87 221 conservative 600946 5p13-p12 growth hormone receptor 266 rs6180 GHR 2690 5 42754996 NM_000163 NP_000154 A/C I544L plus 2123222 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 12 0.5 0.43 0.06 392 6 0.43 0.03 480 8 123 "by doubleHit,freq,cluster" Potentially damaging 1.362 25 Borderline 0.15 2.87 221 conservative 600946 5p13-p12 growth hormone receptor 267 rs6180 GHR 2690 5 42754996 NM_000163 NP_000154 A/C I544L plus 2123222 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 92 0.47 0.43 0.06 392 6 0.43 0.03 480 8 123 "by doubleHit,freq,cluster" Potentially damaging 1.362 25 Borderline 0.15 2.87 221 conservative 600946 5p13-p12 growth hormone receptor 268 rs6180 GHR 2690 5 42754996 NM_000163 NP_000154 A/C I544L plus 2123222 1303 SEQUENOM CEPH CEPH (92) 92 0.47 0.43 0.06 392 6 0.43 0.03 480 8 123 "by doubleHit,freq,cluster" Potentially damaging 1.362 25 Borderline 0.15 2.87 221 conservative 600946 5p13-p12 growth hormone receptor 269 rs6180 GHR 2690 5 42754996 NM_000163 NP_000154 A/C I544L plus 6903813 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.42 0.43 0.06 392 6 0.43 0.03 480 8 123 "by doubleHit,freq,cluster" Potentially damaging 1.362 25 Borderline 0.15 2.87 221 conservative 600946 5p13-p12 growth hormone receptor 270 rs6180 GHR 2690 5 42754996 NM_000163 NP_000154 A/C I544L plus 24423132 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.46 0.43 0.06 392 6 0.43 0.03 480 8 123 "by doubleHit,freq,cluster" Potentially damaging 1.362 25 Borderline 0.15 2.87 221 conservative 600946 5p13-p12 growth hormone receptor 271 rs6181 GHR 2690 5 42735779 NM_000163 NP_000154 A/G R179H plus 7803 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 86 0.03 0.03 0 86 1 116 "HapMap,cluster" Potentially damaging 1.4 25 Borderline 0.13 2.84 53 conservative 600946 5p13-p12 growth hormone receptor 272 rs6182 GHR 2690 5 42754685 NM_000163 NP_000154 G/T C440F plus 7804 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 86 0.1 0.1 0 86 1 0.17 0 48 1 123 "by submitter,freq,cluster" Probably damaging 2.191 25 Potentially intolerant 0.08 3.05 174 radical 600946 5p13-p12 growth hormone receptor 273 rs6183 GHR 2690 5 42754849 NM_000163 NP_000154 A/C P495T plus 7805 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 86 0.03 0.03 0 86 1 52 by freq Probably damaging 2.248 25 Intolerant 0 2.84 222 conservative 600946 5p13-p12 growth hormone receptor 274 rs6184 GHR 2690 5 42755101 NM_000163 NP_000154 A/C P579T plus 7806 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 86 0.1 0.1 0 86 1 0.08 0.09 252 2 116 "by cluster,freq" Potentially damaging 1.473 25 Tolerant 0.29 2.87 211 conservative 600946 5p13-p12 growth hormone receptor 275 rs6185 GNRH1 2796 8 25336717 NM_000825 NP_000816 C/G W16S minus 7807 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 86 0.33 0.25 0.07 406 5 0.43 0.12 1912 7 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.365 6 radical 152760 8p21-p11.2 gonadotropin-releasing hormone 1 (leutinizing-releasing hormone) 276 rs6185 GNRH1 2796 8 25336717 NM_000825 NP_000816 C/G W16S minus 5586544 775 SNP500CANCER CAUC1 Caucasian (31) 60 0.3 0.25 0.07 406 5 0.43 0.12 1912 7 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.365 6 radical 152760 8p21-p11.2 gonadotropin-releasing hormone 1 (leutinizing-releasing hormone) 277 rs6185 GNRH1 2796 8 25336717 NM_000825 NP_000816 C/G W16S minus 6731916 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.23 0.25 0.07 406 5 0.43 0.12 1912 7 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.365 6 radical 152760 8p21-p11.2 gonadotropin-releasing hormone 1 (leutinizing-releasing hormone) 278 rs6185 GNRH1 2796 8 25336717 NM_000825 NP_000816 C/G W16S minus 6731916 1303 SEQUENOM CEPH CEPH (92) 92 0.19 0.25 0.07 406 5 0.43 0.12 1912 7 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.365 6 radical 152760 8p21-p11.2 gonadotropin-releasing hormone 1 (leutinizing-releasing hormone) 279 rs6185 GNRH1 2796 8 25336717 NM_000825 NP_000816 C/G W16S minus 24053467 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.17 0.25 0.07 406 5 0.43 0.12 1912 7 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.365 6 radical 152760 8p21-p11.2 gonadotropin-releasing hormone 1 (leutinizing-releasing hormone) 280 rs6190 NR3C1 2908 5 142760530 NM_000176 NP_000167 A/G R23K minus 14865729 693 EGP_SNPS PDR90 NIHPDR 152 0.01 0.01 0 152 1 119 "by cluster,freq" Potentially damaging 1.293 19 conservative 138040 5q31 "nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor)" 281 rs6192 NR3C1 2908 5 142760405 NM_000176 NP_000167 G/T F65V minus 7814 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 86 0.03 0.02 0.01 238 2 119 "HapMap,cluster" Probably damaging 1.999 22 conservative 138040 5q31 "nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor)" 282 rs6192 NR3C1 2908 5 142760405 NM_000176 NP_000167 G/T F65V minus 14865730 693 EGP_SNPS PDR90 NIHPDR 152 0.01 0.02 0.01 238 2 119 "HapMap,cluster" Probably damaging 1.999 22 conservative 138040 5q31 "nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor)" 283 rs6195 NR3C1 2908 5 142759510 NM_000176 NP_000167 A/G N363S minus 7817 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 86 0.03 0.03 0.02 230 3 0.02 0 646 2 120 "HapMap,freq,cluster" Potentially damaging 1.493 23 Tolerant 0.89 2.84 57 conservative 138040 5q31 "nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor)" 284 rs6195 NR3C1 2908 5 142759510 NM_000176 NP_000167 A/G N363S minus 7817 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.02 0.03 0.02 230 3 0.02 0 646 2 120 "HapMap,freq,cluster" Potentially damaging 1.493 23 Tolerant 0.89 2.84 57 conservative 138040 5q31 "nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor)" 285 rs6195 NR3C1 2908 5 142759510 NM_000176 NP_000167 A/G N363S minus 7817 902 AFFY Caucasian 24 0.08 0.03 0.02 230 3 0.02 0 646 2 120 "HapMap,freq,cluster" Potentially damaging 1.493 23 Tolerant 0.89 2.84 57 conservative 138040 5q31 "nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor)" 286 rs6201 HSD3B1 3283 1 119766257 NM_000862 NP_000853 A/G I79V plus 24811836 1303 SEQUENOM CEPH CEPH (92) 184 0.47 0.47 0 184 1 0.12 0.08 338 4 123 "by cluster,freq" Benign 0.16 29 Tolerant 1 2.84 40 conservative 109715 1p13.1 "hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1" 287 rs6205 HSD3B1 3283 1 119769044 NM_000862 NP_000853 C/T F286L plus 7827 1303 SEQUENOM CEPH CEPH (92) 92 0.07 0.07 0 92 1 123 by freq Potentially damaging 1.441 30 Tolerant 1 2.85 39 conservative 109715 1p13.1 "hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1" 288 rs6211 HSD3B2 3284 1 119674220 NM_000198 NP_000189 C/G E94Q plus 7833 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 86 0.03 0.11 0.11 178 2 0.02 0.02 250 2 113 "by cluster,freq" Benign 0.634 30 Tolerant 1 2.91 40 conservative 201810 1p13.1 "hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 2" 289 rs6211 HSD3B2 3284 1 119674220 NM_000198 NP_000189 C/G E94Q plus 5586599 1303 SEQUENOM CEPH CEPH (92) 92 0.18 0.11 0.11 178 2 0.02 0.02 250 2 113 "by cluster,freq" Benign 0.634 30 Tolerant 1 2.91 40 conservative 201810 1p13.1 "hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 2" 290 rs6232 PCSK1 5122 5 95777541 NM_000439 NP_000430 A/G N221D minus 7854 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 86 0.03 0.09 0.09 344 4 123 "HapMap,freq" Benign 0.371 10 Tolerant 0.23 2.78 108 conservative 162150 5q15-q21 proprotein convertase subtilisin/kexin type 1 291 rs6232 PCSK1 5122 5 95777541 NM_000439 NP_000430 A/G N221D minus 7854 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.04 0.09 0.09 344 4 123 "HapMap,freq" Benign 0.371 10 Tolerant 0.23 2.78 108 conservative 162150 5q15-q21 proprotein convertase subtilisin/kexin type 1 292 rs6232 PCSK1 5122 5 95777541 NM_000439 NP_000430 A/G N221D minus 7854 1303 SEQUENOM CEPH CEPH (92) 92 0.22 0.09 0.09 344 4 123 "HapMap,freq" Benign 0.371 10 Tolerant 0.23 2.78 108 conservative 162150 5q15-q21 proprotein convertase subtilisin/kexin type 1 293 rs6232 PCSK1 5122 5 95777541 NM_000439 NP_000430 A/G N221D minus 24445734 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.09 0.09 344 4 123 "HapMap,freq" Benign 0.371 10 Tolerant 0.23 2.78 108 conservative 162150 5q15-q21 proprotein convertase subtilisin/kexin type 1 294 rs6234 PCSK1 5122 5 95754730 NM_000439 NP_000430 C/G Q665E minus 7856 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 84 0.33 0.3 0.07 224 3 0.21 0.14 94 2 123 "by cluster,freq" Benign 0 9 conservative 162150 5q15-q21 proprotein convertase subtilisin/kexin type 1 295 rs6234 PCSK1 5122 5 95754730 NM_000439 NP_000430 C/G Q665E minus 7856 1303 SEQUENOM CEPH CEPH (92) 92 0.33 0.3 0.07 224 3 0.21 0.14 94 2 123 "by cluster,freq" Benign 0 9 conservative 162150 5q15-q21 proprotein convertase subtilisin/kexin type 1 296 rs6234 PCSK1 5122 5 95754730 NM_000439 NP_000430 C/G Q665E minus 24001977 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.19 0.3 0.07 224 3 0.21 0.14 94 2 123 "by cluster,freq" Benign 0 9 conservative 162150 5q15-q21 proprotein convertase subtilisin/kexin type 1 297 rs6235 PCSK1 5122 5 95754654 NM_000439 NP_000430 C/G S690T minus 7857 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 86 0.1 0.25 0.13 346 4 0.21 0.14 94 2 123 "HapMap,submitter,freq,cluster" Borderline 1.19 7 moderately conservative 162150 5q15-q21 proprotein convertase subtilisin/kexin type 1 298 rs6235 PCSK1 5122 5 95754654 NM_000439 NP_000430 C/G S690T minus 7857 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.27 0.25 0.13 346 4 0.21 0.14 94 2 123 "HapMap,submitter,freq,cluster" Borderline 1.19 7 moderately conservative 162150 5q15-q21 proprotein convertase subtilisin/kexin type 1 299 rs6235 PCSK1 5122 5 95754654 NM_000439 NP_000430 C/G S690T minus 7857 1303 SEQUENOM CEPH CEPH (92) 92 0.4 0.25 0.13 346 4 0.21 0.14 94 2 123 "HapMap,submitter,freq,cluster" Borderline 1.19 7 moderately conservative 162150 5q15-q21 proprotein convertase subtilisin/kexin type 1 300 rs6235 PCSK1 5122 5 95754654 NM_000439 NP_000430 C/G S690T minus 24001971 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.19 0.25 0.13 346 4 0.21 0.14 94 2 123 "HapMap,submitter,freq,cluster" Borderline 1.19 7 moderately conservative 162150 5q15-q21 proprotein convertase subtilisin/kexin type 1 301 rs6259 SHBG 6462 17 7477252 NM_001040 NP_001031 A/G D356N plus 5586913 775 SNP500CANCER CAUC1 Caucasian (31) 60 0.1 0.2 0.11 152 2 0.08 0.02 340 4 123 "by cluster,freq" Benign 0.164 11 Tolerant 0.46 2.75 16 conservative 182205 17p13-p12 sex hormone-binding globulin 302 rs6259 SHBG 6462 17 7477252 NM_001040 NP_001031 A/G D356N plus 5586913 1303 SEQUENOM CEPH CEPH (92) 92 0.26 0.2 0.11 152 2 0.08 0.02 340 4 123 "by cluster,freq" Benign 0.164 11 Tolerant 0.46 2.75 16 conservative 182205 17p13-p12 sex hormone-binding globulin 303 rs6260 SHBG 6462 17 7474289 NM_001040 NP_001031 A/G R25H plus 7883 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 86 0.1 0.1 0 86 1 0.06 0.07 252 2 118 "HapMap,freq,cluster" Probably damaging 2.284 6 conservative 182205 17p13-p12 sex hormone-binding globulin 304 rs6262 DDC 1644 7 50370129 NM_000790 NP_000781 C/T P210L minus 16361341 693 EGP_SNPS PDR90 NIHPDR 180 0.01 0.01 0 180 1 121 "HapMap,freq,cluster" Probably damaging 2.224 106 Intolerant 0.01 2.82 229 moderately conservative 107930 7p11 dopa decarboxylase (aromatic L-amino acid decarboxylase) 305 rs6263 DDC 1644 7 50370109 NM_000790 NP_000781 A/G M217V minus 16361342 693 EGP_SNPS PDR90 NIHPDR 180 0.03 0.03 0.01 294 2 121 "HapMap,freq,cluster" Borderline 1.014 106 Potentially intolerant 0.06 2.82 229 conservative 107930 7p11 dopa decarboxylase (aromatic L-amino acid decarboxylase) 306 rs6263 DDC 1644 7 50370109 NM_000790 NP_000781 A/G M217V minus 16361342 885 TSC-CSHL HapMap-CEPH-30-trios 114 0.04 0.03 0.01 294 2 121 "HapMap,freq,cluster" Borderline 1.014 106 Potentially intolerant 0.06 2.82 229 conservative 107930 7p11 dopa decarboxylase (aromatic L-amino acid decarboxylase) 307 rs6266 CNTF 1270 11 58148513 NM_000614 NP_000605 A/G H182R plus 7890 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 74 0.03 0.03 0 74 1 52 by freq Probably damaging 2.24 7 Tolerant 0.45 3 16 conservative 118945 11q12.2 ciliary neurotrophic factor 308 rs6270 COMT 1312 22 18324704 NM_000754 NP_000745 C/G C34S plus 7895 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 70 0.33 0.33 0 70 1 113 "HapMap,cluster" Benign 0.027 5 moderately radical 116790 22q11.21 catechol-O-methyltransferase 309 rs6271 DBH 1621 9 133551828 NM_000787 NP_000778 C/T R535C plus 7898 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 74 0.1 0.07 0.04 166 2 123 "by submitter,freq,cluster" Probably damaging 2.278 11 Intolerant 0.05 2.81 26 radical 223360 9q34 dopamine beta-hydroxylase (dopamine beta-monooxygenase) 310 rs6271 DBH 1621 9 133551828 NM_000787 NP_000778 C/T R535C plus 7898 1303 SEQUENOM CEPH CEPH (92) 92 0.04 0.07 0.04 166 2 123 "by submitter,freq,cluster" Probably damaging 2.278 11 Intolerant 0.05 2.81 26 radical 223360 9q34 dopamine beta-hydroxylase (dopamine beta-monooxygenase) 311 rs6330 NGFB 4803 1 115541355 NM_002506 NP_002497 C/T A35V minus 7958 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 74 0.33 0.42 0.07 332 5 0.17 0.02 968 2 120 "HapMap,doubleHit,submitter,freq,cluster" Borderline 1.034 30 moderately conservative 162030 1p13.1 "nerve growth factor, beta polypeptide" 312 rs6330 NGFB 4803 1 115541355 NM_002506 NP_002497 C/T A35V minus 4044499 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.48 0.42 0.07 332 5 0.17 0.02 968 2 120 "HapMap,doubleHit,submitter,freq,cluster" Borderline 1.034 30 moderately conservative 162030 1p13.1 "nerve growth factor, beta polypeptide" 313 rs6330 NGFB 4803 1 115541355 NM_002506 NP_002497 C/T A35V minus 4044499 1303 SEQUENOM CEPH CEPH (92) 92 0.4 0.42 0.07 332 5 0.17 0.02 968 2 120 "HapMap,doubleHit,submitter,freq,cluster" Borderline 1.034 30 moderately conservative 162030 1p13.1 "nerve growth factor, beta polypeptide" 314 rs6330 NGFB 4803 1 115541355 NM_002506 NP_002497 C/T A35V minus 15356259 847 IIPGA-WEISS-MARTINEZ E-0 CEPH 40 0.45 0.42 0.07 332 5 0.17 0.02 968 2 120 "HapMap,doubleHit,submitter,freq,cluster" Borderline 1.034 30 moderately conservative 162030 1p13.1 "nerve growth factor, beta polypeptide" 315 rs6330 NGFB 4803 1 115541355 NM_002506 NP_002497 C/T A35V minus 15356259 848 IIPGA-WEISS-MARTINEZ E-1 CEPH 6 0.33 0.42 0.07 332 5 0.17 0.02 968 2 120 "HapMap,doubleHit,submitter,freq,cluster" Borderline 1.034 30 moderately conservative 162030 1p13.1 "nerve growth factor, beta polypeptide" 316 rs6336 NTRK1 4914 1 153661991 NM_002529 NP_002520 C/T H604Y plus 7964 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 74 0.03 0.05 0.03 348 3 123 by freq Possibly damaging 1.834 7 Intolerant 0.01 2.92 33 moderately conservative 191315 1q21-q22 "neurotrophic tyrosine kinase, receptor, type 1" 317 rs6336 NTRK1 4914 1 153661991 NM_002529 NP_002520 C/T H604Y plus 6416724 1303 SEQUENOM CEPH CEPH (92) 92 0.02 0.05 0.03 348 3 123 by freq Possibly damaging 1.834 7 Intolerant 0.01 2.92 33 moderately conservative 191315 1q21-q22 "neurotrophic tyrosine kinase, receptor, type 1" 318 rs6336 NTRK1 4914 1 153661991 NM_002529 NP_002520 C/T H604Y plus 28447275 914 HG_BONN_CNS_SNPS EURO96 European 182 0.07 0.05 0.03 348 3 123 by freq Possibly damaging 1.834 7 Intolerant 0.01 2.92 33 moderately conservative 191315 1q21-q22 "neurotrophic tyrosine kinase, receptor, type 1" 319 rs6339 NTRK1 4914 1 153662019 NM_002529 NP_002520 G/T G613V plus 7967 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 74 0.03 0.06 0.03 256 2 123 by freq Possibly damaging 1.497 7 Potentially intolerant 0.1 2.98 25 moderately radical 191315 1q21-q22 "neurotrophic tyrosine kinase, receptor, type 1" 320 rs6339 NTRK1 4914 1 153662019 NM_002529 NP_002520 G/T G613V plus 28447276 914 HG_BONN_CNS_SNPS EURO96 European 182 0.07 0.06 0.03 256 2 123 by freq Possibly damaging 1.497 7 Potentially intolerant 0.1 2.98 25 moderately radical 191315 1q21-q22 "neurotrophic tyrosine kinase, receptor, type 1" 321 rs6405 CYP11B1 1584 8 143958203 NM_000497 NP_000488 A/G C10Y minus 8043 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 86 0.03 0.03 0 86 1 52 by freq Tolerant 1 3.16 26 radical 202010 8q21 "cytochrome P450, family 11, subfamily B, polypeptide 1" 322 rs6407 CYP11B1 1584 8 143954209 NM_000497 NP_000488 A/G A348T minus 8046 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 86 0.03 0.03 0 86 1 52 by freq Borderline 1.168 36 Borderline 0.15 2.77 41 moderately conservative 202010 8q21 "cytochrome P450, family 11, subfamily B, polypeptide 1" 323 rs6438 CYP11B2 1585 8 143996174 NM_000498 NP_000489 A/G A29T minus 8081 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 84 0.03 0.03 0 84 1 0.04 0 46 1 123 "by cluster,freq" Benign 0.221 36 Tolerant 0.71 2.9 29 moderately conservative 124080 8q21-q22 "cytochrome P450, family 11, subfamily B, polypeptide 2" 324 rs6472 CYP21A2 1589 6 32115828 NM_000500 NP_000491 C/G S269T plus 8123 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 86 0.33 0.22 0.13 362 3 0.1 0 1478 1 123 "by cluster,freq" Borderline 1.001 23 Potentially intolerant 0.1 2.79 33 moderately conservative 201910 6p21.3 "cytochrome P450, family 21, subfamily A, polypeptide 2" 325 rs6472 CYP21A2 1589 6 32115828 NM_000500 NP_000491 C/G S269T plus 13097014 1303 SEQUENOM CEPH CEPH (92) 92 0.04 0.22 0.13 362 3 0.1 0 1478 1 123 "by cluster,freq" Borderline 1.001 23 Potentially intolerant 0.1 2.79 33 moderately conservative 201910 6p21.3 "cytochrome P450, family 21, subfamily A, polypeptide 2" 326 rs6472 CYP21A2 1589 6 32115828 NM_000500 NP_000491 C/G S269T plus 24796289 1303 SEQUENOM CEPH CEPH (92) 184 0.25 0.22 0.13 362 3 0.1 0 1478 1 123 "by cluster,freq" Borderline 1.001 23 Potentially intolerant 0.1 2.79 33 moderately conservative 201910 6p21.3 "cytochrome P450, family 21, subfamily A, polypeptide 2" 327 rs6474 CYP21A2 1589 6 32114865 NM_000500 NP_000491 A/G R103K plus 8125 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 84 0.33 0.33 0 84 1 113 "by doubleHit,freq,cluster" Benign 0.118 14 Tolerant 0.63 2.81 27 conservative 201910 6p21.3 "cytochrome P450, family 21, subfamily A, polypeptide 2" 328 rs6476 CYP21A2 1589 6 32115572 NM_000500 NP_000491 A/T M240K plus 8127 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 86 0.03 0.03 0 86 1 120 "by doubleHit,freq,cluster" Benign 0.284 23 Tolerant 1 2.79 33 moderately conservative 201910 6p21.3 "cytochrome P450, family 21, subfamily A, polypeptide 2" 329 rs6525 BMP8A 353500 1 39657177 NM_181809 NP_861525 A/G R293H plus 8185 508 WIAF-CSNP WIAF-CSNP-MITOGPOP1 "Europeans (20), Asians (10) and African-Americans (10)" 38 0.33 0.31 0.01 318 3 121 "by doubleHit,freq,cluster" conservative 1p34.2 bone morphogenetic protein 8a 330 rs6525 BMP8A 353500 1 39657177 NM_181809 NP_861525 A/G R293H plus 17934 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.31 0.31 0.01 318 3 121 "by doubleHit,freq,cluster" conservative 1p34.2 bone morphogenetic protein 8a 331 rs6525 BMP8A 353500 1 39657177 NM_181809 NP_861525 A/G R293H plus 20433475 1303 SEQUENOM CEPH CEPH (92) 92 0.31 0.31 0.01 318 3 121 "by doubleHit,freq,cluster" conservative 1p34.2 bone morphogenetic protein 8a 332 rs6577 GSTA2 2939 6 52723374 NM_000846 NP_000837 A/C E210A minus 869782 506 NCBI NIHPDR NIHPDR 78 0.29 0.18 0.15 170 2 120 "by doubleHit,submitter,freq,cluster" Benign 0.802 61 Tolerant 0.21 2.86 64 moderately radical 138360 6p12.1 glutathione S-transferase A2 333 rs6577 GSTA2 2939 6 52723374 NM_000846 NP_000837 A/C E210A minus 3671245 1303 SEQUENOM CEPH CEPH (92) 92 0.08 0.18 0.15 170 2 120 "by doubleHit,submitter,freq,cluster" Benign 0.802 61 Tolerant 0.21 2.86 64 moderately radical 138360 6p12.1 glutathione S-transferase A2 334 rs6647 SERPINA1 5265 14 93917168 NM_000295 NP_000286 C/T V237A minus 20192 523 WIAF-CSNP WIAF-CSNP-MITOGPOP4 "Europeans (20), Asians (10) and African-Americans (10)" 38 0.33 0.28 0.03 178 3 0.27 0.3 94 2 123 "by doubleHit,freq,cluster" Tolerant 0.48 2.75 79 moderately conservative 107400 14q32.1 "serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1" 335 rs6647 SERPINA1 5265 14 93917168 NM_000295 NP_000286 C/T V237A minus 1875346 1303 SEQUENOM CEPH CEPH (92) 92 0.27 0.28 0.03 178 3 0.27 0.3 94 2 123 "by doubleHit,freq,cluster" Tolerant 0.48 2.75 79 moderately conservative 107400 14q32.1 "serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1" 336 rs6647 SERPINA1 5265 14 93917168 NM_000295 NP_000286 C/T V237A minus 23648078 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.27 0.28 0.03 178 3 0.27 0.3 94 2 123 "by doubleHit,freq,cluster" Tolerant 0.48 2.75 79 moderately conservative 107400 14q32.1 "serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1" 337 rs6791 STXBP2 6813 19 7618277 NM_006949 NP_008880 A/G I526V plus 8516 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.26 0.28 0.05 324 3 0.18 0.04 88 2 123 "by doubleHit,freq,cluster" Benign 0.106 26 conservative 601717 19p13.3-p13.2 syntaxin binding protein 2 338 rs6791 STXBP2 6813 19 7618277 NM_006949 NP_008880 A/G I526V plus 1414714 1303 SEQUENOM CEPH CEPH (92) 92 0.26 0.28 0.05 324 3 0.18 0.04 88 2 123 "by doubleHit,freq,cluster" Benign 0.106 26 conservative 601717 19p13.3-p13.2 syntaxin binding protein 2 339 rs6791 STXBP2 6813 19 7618277 NM_006949 NP_008880 A/G I526V plus 24417641 1371 PERLEGEN AFD_EUR_PANEL European American (24) 44 0.39 0.28 0.05 324 3 0.18 0.04 88 2 123 "by doubleHit,freq,cluster" Benign 0.106 26 conservative 601717 19p13.3-p13.2 syntaxin binding protein 2 340 rs6794 EXOSC7 23016 3 45027779 NM_015004 NP_055819 C/G V274L plus 8519 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.5 0.49 0.01 354 3 0.12 0 1474 1 120 "HapMap,doubleHit,freq,cluster" Borderline 1.21 6 conservative 606488 3p21.32 exosome component 7 341 rs6794 EXOSC7 23016 3 45027779 NM_015004 NP_055819 C/G V274L plus 10058733 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.48 0.49 0.01 354 3 0.12 0 1474 1 120 "HapMap,doubleHit,freq,cluster" Borderline 1.21 6 conservative 606488 3p21.32 exosome component 7 342 rs6794 EXOSC7 23016 3 45027779 NM_015004 NP_055819 C/G V274L plus 10058733 1303 SEQUENOM CEPH CEPH (92) 46 0.5 0.49 0.01 354 3 0.12 0 1474 1 120 "HapMap,doubleHit,freq,cluster" Borderline 1.21 6 conservative 606488 3p21.32 exosome component 7 343 rs6834 KARS 3735 16 74219304 NM_005548 NP_005539 C/G T595S minus 12357600 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.05 0.03 0.03 212 2 0.33 0 84 1 120 "HapMap,doubleHit,freq,cluster" Borderline 1.107 9 moderately conservative 601421 16q23-q24 lysyl-tRNA synthetase 344 rs6834 KARS 3735 16 74219304 NM_005548 NP_005539 C/G T595S minus 12357600 1303 SEQUENOM CEPH CEPH (92) 92 0.01 0.03 0.03 212 2 0.33 0 84 1 120 "HapMap,doubleHit,freq,cluster" Borderline 1.107 9 moderately conservative 601421 16q23-q24 lysyl-tRNA synthetase 345 rs6901 PITRM1 10531 10 3170227 NM_014889 NP_055704 A/G Q1037R minus 8650 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.28 0.3 0.05 389 4 0.25 0.02 1692 5 123 "by doubleHit,freq,cluster" Potentially damaging 1.355 8 conservative 10p15.3 pitrilysin metalloproteinase 1 346 rs6901 PITRM1 10531 10 3170227 NM_014889 NP_055704 A/G Q1037R minus 3349913 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 60 0.33 0.3 0.05 389 4 0.25 0.02 1692 5 123 "by doubleHit,freq,cluster" Potentially damaging 1.355 8 conservative 10p15.3 pitrilysin metalloproteinase 1 347 rs6901 PITRM1 10531 10 3170227 NM_014889 NP_055704 A/G Q1037R minus 3349913 1303 SEQUENOM CEPH CEPH (92) 93 0.28 0.3 0.05 389 4 0.25 0.02 1692 5 123 "by doubleHit,freq,cluster" Potentially damaging 1.355 8 conservative 10p15.3 pitrilysin metalloproteinase 1 348 rs6901 PITRM1 10531 10 3170227 NM_014889 NP_055704 A/G Q1037R minus 24294922 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.4 0.3 0.05 389 4 0.25 0.02 1692 5 123 "by doubleHit,freq,cluster" Potentially damaging 1.355 8 conservative 10p15.3 pitrilysin metalloproteinase 1 349 rs6940 IFI16 3428 1 155837741 NM_005531 NP_005522 A/T T723S plus 3127046 1303 SEQUENOM CEPH CEPH (92) 92 0.1 0.1 0 92 1 120 "by doubleHit,freq,cluster" moderately conservative 147586 1q22 "interferon, gamma-inducible protein 16" 350 rs6972 BZRP 706 22 41883470 NM_000714 NP_000705 A/G R162H plus 8733 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.33 0.27 0.09 544 5 0.14 0.08 652 7 120 "by doubleHit,freq,cluster" Benign 0.32 10 conservative 109610 22q13.31 benzodiazapine receptor (peripheral) 351 rs6972 BZRP 706 22 41883470 NM_000714 NP_000705 A/G R162H plus 3176163 619 WICVAR MITOGPOP6 CORIELL Mixed 34 0.03 0.27 0.09 544 5 0.14 0.08 652 7 120 "by doubleHit,freq,cluster" Benign 0.32 10 conservative 109610 22q13.31 benzodiazapine receptor (peripheral) 352 rs6972 BZRP 706 22 41883470 NM_000714 NP_000705 A/G R162H plus 5169438 1303 SEQUENOM CEPH CEPH (92) 92 0.33 0.27 0.09 544 5 0.14 0.08 652 7 120 "by doubleHit,freq,cluster" Benign 0.32 10 conservative 109610 22q13.31 benzodiazapine receptor (peripheral) 353 rs6972 BZRP 706 22 41883470 NM_000714 NP_000705 A/G R162H plus 7986212 775 SNP500CANCER CAUC1 Caucasian (31) 60 0.18 0.27 0.09 544 5 0.14 0.08 652 7 120 "by doubleHit,freq,cluster" Benign 0.32 10 conservative 109610 22q13.31 benzodiazapine receptor (peripheral) 354 rs6972 BZRP 706 22 41883470 NM_000714 NP_000705 A/G R162H plus 12704282 693 EGP_SNPS PDR90 NIHPDR 170 0.24 0.27 0.09 544 5 0.14 0.08 652 7 120 "by doubleHit,freq,cluster" Benign 0.32 10 conservative 109610 22q13.31 benzodiazapine receptor (peripheral) 355 rs7041 GC 2638 4 72983369 NM_000583 NP_000574 G/T D432E minus 6903804 775 SNP500CANCER CAUC1 Caucasian (31) 60 0.42 0.42 0.02 1073 3 0.34 0.1 344 4 121 "by doubleHit,submitter,freq,cluster" Benign 0.113 9 Tolerant 1 2.75 20 conservative 139200 4q12-q13 group-specific component (vitamin D binding protein) 356 rs7041 GC 2638 4 72983369 NM_000583 NP_000574 G/T D432E minus 6903804 1303 SEQUENOM CEPH CEPH (92) 92 0.47 0.42 0.02 1073 3 0.34 0.1 344 4 121 "by doubleHit,submitter,freq,cluster" Benign 0.113 9 Tolerant 1 2.75 20 conservative 139200 4q12-q13 group-specific component (vitamin D binding protein) 357 rs7041 GC 2638 4 72983369 NM_000583 NP_000574 G/T D432E minus 12587289 928 IBARROSO ELY UK (Ely region of East Anglia) 921 0.41 0.42 0.02 1073 3 0.34 0.1 344 4 121 "by doubleHit,submitter,freq,cluster" Benign 0.113 9 Tolerant 1 2.75 20 conservative 139200 4q12-q13 group-specific component (vitamin D binding protein) 358 rs7185 FARSLB 10056 2 223262112 NM_005687 NP_005678 C/T V585I plus 14504693 1303 SEQUENOM CEPH CEPH (92) 92 0.07 0.09 0.04 140 2 0.03 0.05 1552 3 123 "by doubleHit,submitter,freq,cluster" Benign 0.012 13 conservative 2q36.1-q36.2 "phenylalanine-tRNA synthetase-like, beta subunit" 359 rs7185 FARSLB 10056 2 223262112 NM_005687 NP_005678 C/T V585I plus 23326076 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.09 0.04 140 2 0.03 0.05 1552 3 123 "by doubleHit,submitter,freq,cluster" Benign 0.012 13 conservative 2q36.1-q36.2 "phenylalanine-tRNA synthetase-like, beta subunit" 360 rs7251 IRF3 3661 19 54854721 NM_001571 NP_001562 C/G S427T minus 9071 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.31 0.33 0.05 342 3 123 "by doubleHit,freq,cluster" moderately conservative 603734 19q13.3-q13.4 interferon regulatory factor 3 361 rs7251 IRF3 3661 19 54854721 NM_001571 NP_001562 C/G S427T minus 1321615 1303 SEQUENOM CEPH CEPH (92) 92 0.31 0.33 0.05 342 3 123 "by doubleHit,freq,cluster" moderately conservative 603734 19q13.3-q13.4 interferon regulatory factor 3 362 rs7251 IRF3 3661 19 54854721 NM_001571 NP_001562 C/G S427T minus 3177824 619 WICVAR MITOGPOP6 CORIELL Mixed 62 0.42 0.33 0.05 342 3 123 "by doubleHit,freq,cluster" moderately conservative 603734 19q13.3-q13.4 interferon regulatory factor 3 363 rs7412 APOE 348 19 50103919 NM_000041 NP_000032 C/T R176C plus 870165 563 DEBNICK MDECODE-1 European-Americans 48 0.19 0.1 0.05 1970 4 0.04 0 48 1 120 "by doubleHit,freq,cluster" Benign 0.035 29 Intolerant 0.02 2.79 33 radical 107741 19q13.2 apolipoprotein E 364 rs7412 APOE 348 19 50103919 NM_000041 NP_000032 C/T R176C plus 870165 564 DEBNICK MDECODE-2 Finnish 48 0.04 0.1 0.05 1970 4 0.04 0 48 1 120 "by doubleHit,freq,cluster" Benign 0.035 29 Intolerant 0.02 2.79 33 radical 107741 19q13.2 apolipoprotein E 365 rs7412 APOE 348 19 50103919 NM_000041 NP_000032 C/T R176C plus 12568612 887 CUORCGL AMERICAN CAUCASIANS American Caucasians 1782 0.09 0.1 0.05 1970 4 0.04 0 48 1 120 "by doubleHit,freq,cluster" Benign 0.035 29 Intolerant 0.02 2.79 33 radical 107741 19q13.2 apolipoprotein E 366 rs7412 APOE 348 19 50103919 NM_000041 NP_000032 C/T R176C plus 15840556 1303 SEQUENOM CEPH CEPH (92) 92 0.28 0.1 0.05 1970 4 0.04 0 48 1 120 "by doubleHit,freq,cluster" Benign 0.035 29 Intolerant 0.02 2.79 33 radical 107741 19q13.2 apolipoprotein E 367 rs7483 GSTM3 2947 1 109991743 NM_000849 NP_000840 A/G V224I minus 9353 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.26 0.29 0.06 458 5 0.33 0.13 436 6 123 "by doubleHit,freq,cluster" conservative 138390 1p13.3 glutathione S-transferase M3 (brain) 368 rs7483 GSTM3 2947 1 109991743 NM_000849 NP_000840 A/G V224I minus 2378699 1303 SEQUENOM CEPH CEPH (92) 92 0.26 0.29 0.06 458 5 0.33 0.13 436 6 123 "by doubleHit,freq,cluster" conservative 138390 1p13.3 glutathione S-transferase M3 (brain) 369 rs7483 GSTM3 2947 1 109991743 NM_000849 NP_000840 A/G V224I minus 3172582 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 68 0.41 0.29 0.06 458 5 0.33 0.13 436 6 123 "by doubleHit,freq,cluster" conservative 138390 1p13.3 glutathione S-transferase M3 (brain) 370 rs7483 GSTM3 2947 1 109991743 NM_000849 NP_000840 A/G V224I minus 6903821 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.34 0.29 0.06 458 5 0.33 0.13 436 6 123 "by doubleHit,freq,cluster" conservative 138390 1p13.3 glutathione S-transferase M3 (brain) 371 rs7483 GSTM3 2947 1 109991743 NM_000849 NP_000840 A/G V224I minus 23868204 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.27 0.29 0.06 458 5 0.33 0.13 436 6 123 "by doubleHit,freq,cluster" conservative 138390 1p13.3 glutathione S-transferase M3 (brain) 372 rs7535 SRP14 6727 15 38115867 NM_003134 NP_003125 C/G P124A minus 3177688 619 WICVAR MITOGPOP6 CORIELL Mixed 44 0.23 0.09 0.12 162 2 0.28 0 1482 1 121 "HapMap,doubleHit,freq,cluster" conservative 600708 15q22 signal recognition particle 14kDa (homologous Alu RNA binding protein) 373 rs7535 SRP14 6727 15 38115867 NM_003134 NP_003125 C/G P124A minus 4092989 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.04 0.09 0.12 162 2 0.28 0 1482 1 121 "HapMap,doubleHit,freq,cluster" conservative 600708 15q22 signal recognition particle 14kDa (homologous Alu RNA binding protein) 374 rs7571 ADPRTL1 143 13 23898617 NM_006437 NP_006428 C/G A1656P minus 6903629 775 SNP500CANCER CAUC1 Caucasian (31) 58 0.48 0.48 0 58 1 0.46 0.05 342 4 119 "by doubleHit,freq,cluster" conservative 607519 13q11 ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1 375 rs7799 ELF1 1997 13 40431052 NM_172373 NP_758961 A/G N58S minus 9720 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.32 0.32 0 280 2 123 "by doubleHit,submitter,freq,cluster" Benign 0.575 5 Borderline 0.16 2.97 21 conservative 189973 13q13 E74-like factor 1 (ets domain transcription factor) 376 rs7799 ELF1 1997 13 40431052 NM_172373 NP_758961 A/G N58S minus 2934168 1303 SEQUENOM CEPH CEPH (92) 92 0.32 0.32 0 280 2 123 "by doubleHit,submitter,freq,cluster" Benign 0.575 5 Borderline 0.16 2.97 21 conservative 189973 13q13 E74-like factor 1 (ets domain transcription factor) 377 rs7825 OVGP1 5016 1 111669139 NM_002557 NP_002548 C/G E676Q plus 9747 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.4 0.4 0.07 364 5 0.23 0.05 1639 6 123 "by doubleHit,submitter,freq,cluster" conservative 603578 1p13 "oviductal glycoprotein 1, 120kDa (mucin 9, oviductin)" 378 rs7825 OVGP1 5016 1 111669139 NM_002557 NP_002548 C/G E676Q plus 2620723 1303 SEQUENOM CEPH CEPH (92) 92 0.4 0.4 0.07 364 5 0.23 0.05 1639 6 123 "by doubleHit,submitter,freq,cluster" conservative 603578 1p13 "oviductal glycoprotein 1, 120kDa (mucin 9, oviductin)" 379 rs7825 OVGP1 5016 1 111669139 NM_002557 NP_002548 C/G E676Q plus 16333801 902 AFFY Caucasian 24 0.42 0.4 0.07 364 5 0.23 0.05 1639 6 123 "by doubleHit,submitter,freq,cluster" conservative 603578 1p13 "oviductal glycoprotein 1, 120kDa (mucin 9, oviductin)" 380 rs7825 OVGP1 5016 1 111669139 NM_002557 NP_002548 C/G E676Q plus 16333801 904 AFFY CEPH 12 0.08 0.4 0.07 364 5 0.23 0.05 1639 6 123 "by doubleHit,submitter,freq,cluster" conservative 603578 1p13 "oviductal glycoprotein 1, 120kDa (mucin 9, oviductin)" 381 rs7825 OVGP1 5016 1 111669139 NM_002557 NP_002548 C/G E676Q plus 24266714 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.44 0.4 0.07 364 5 0.23 0.05 1639 6 123 "by doubleHit,submitter,freq,cluster" conservative 603578 1p13 "oviductal glycoprotein 1, 120kDa (mucin 9, oviductin)" 382 rs8012 GCDH 2639 19 12871520 NM_013976 NP_039663 A/G Q417R plus 9953 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.26 0.26 0 280 2 121 "by doubleHit,freq,cluster" Potentially intolerant 0.08 2.93 57 conservative 608801 19p13.2 glutaryl-Coenzyme A dehydrogenase 383 rs8012 GCDH 2639 19 12871520 NM_013976 NP_039663 A/G Q417R plus 17615281 1303 SEQUENOM CEPH CEPH (92) 92 0.26 0.26 0 280 2 121 "by doubleHit,freq,cluster" Potentially intolerant 0.08 2.93 57 conservative 608801 19p13.2 glutaryl-Coenzyme A dehydrogenase 384 rs8017 TCEB2 6923 16 2761574 NM_207013 NP_996896 C/T S129N plus 3287771 1303 SEQUENOM CEPH CEPH (92) 46 0.5 0.5 0 46 1 123 "by doubleHit,freq,cluster" conservative 600787 16p12.3 "transcription elongation factor B (SIII), polypeptide 2 (18kDa, elongin B)" 385 rs8207 PPIG 9360 2 170319370 NM_004792 NP_004783 A/G N699D plus 10166 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.2 0.21 0.01 398 3 121 "HapMap,doubleHit,freq,cluster" conservative 606093 2q31.1 peptidyl-prolyl isomerase G (cyclophilin G) 386 rs8207 PPIG 9360 2 170319370 NM_004792 NP_004783 A/G N699D plus 10007638 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.22 0.21 0.01 398 3 121 "HapMap,doubleHit,freq,cluster" conservative 606093 2q31.1 peptidyl-prolyl isomerase G (cyclophilin G) 387 rs8207 PPIG 9360 2 170319370 NM_004792 NP_004783 A/G N699D plus 10007638 1303 SEQUENOM CEPH CEPH (92) 92 0.2 0.21 0.01 398 3 121 "HapMap,doubleHit,freq,cluster" conservative 606093 2q31.1 peptidyl-prolyl isomerase G (cyclophilin G) 388 rs8289 M6PRBP1 10226 19 4810937 NM_005817 NP_005808 A/G I56V minus 10262 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.43 0.4 0.1 324 3 0.4 0.01 1582 3 123 "by doubleHit,freq,cluster" Benign 0.089 6 Tolerant 0.61 2.95 37 conservative 602702 19p13.3 mannose-6-phosphate receptor binding protein 1 389 rs8289 M6PRBP1 10226 19 4810937 NM_005817 NP_005808 A/G I56V minus 3747046 1303 SEQUENOM CEPH CEPH (92) 92 0.43 0.4 0.1 324 3 0.4 0.01 1582 3 123 "by doubleHit,freq,cluster" Benign 0.089 6 Tolerant 0.61 2.95 37 conservative 602702 19p13.3 mannose-6-phosphate receptor binding protein 1 390 rs8289 M6PRBP1 10226 19 4810937 NM_005817 NP_005808 A/G I56V minus 24082489 1371 PERLEGEN AFD_EUR_PANEL European American (24) 44 0.18 0.4 0.1 324 3 0.4 0.01 1582 3 123 "by doubleHit,freq,cluster" Benign 0.089 6 Tolerant 0.61 2.95 37 conservative 602702 19p13.3 mannose-6-phosphate receptor binding protein 1 391 rs8305 POLI 11201 18 50074803 NM_007195 NP_009126 A/G A706T plus 4480077 506 NCBI NIHPDR NIHPDR 122 0.26 0.28 0.06 560 5 0.17 0.08 94 2 123 "HapMap,doubleHit,freq,cluster" Benign 0.9 5 moderately conservative 605252 18q21.1 polymerase (DNA directed) iota 392 rs8305 POLI 11201 18 50074803 NM_007195 NP_009126 A/G A706T plus 4916789 693 EGP_SNPS PDR90 NIHPDR 178 0.24 0.28 0.06 560 5 0.17 0.08 94 2 123 "HapMap,doubleHit,freq,cluster" Benign 0.9 5 moderately conservative 605252 18q21.1 polymerase (DNA directed) iota 393 rs8305 POLI 11201 18 50074803 NM_007195 NP_009126 A/G A706T plus 4916789 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.26 0.28 0.06 560 5 0.17 0.08 94 2 123 "HapMap,doubleHit,freq,cluster" Benign 0.9 5 moderately conservative 605252 18q21.1 polymerase (DNA directed) iota 394 rs8305 POLI 11201 18 50074803 NM_007195 NP_009126 A/G A706T plus 4916789 1303 SEQUENOM CEPH CEPH (92) 92 0.38 0.28 0.06 560 5 0.17 0.08 94 2 123 "HapMap,doubleHit,freq,cluster" Benign 0.9 5 moderately conservative 605252 18q21.1 polymerase (DNA directed) iota 395 rs8305 POLI 11201 18 50074803 NM_007195 NP_009126 A/G A706T plus 24531273 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.33 0.28 0.06 560 5 0.17 0.08 94 2 123 "HapMap,doubleHit,freq,cluster" Benign 0.9 5 moderately conservative 605252 18q21.1 polymerase (DNA directed) iota 396 rs8337 UBD 10537 6 29631655 NM_006398 NP_006389 C/G C160S minus 10314 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.28 0.24 0.07 604 4 0.08 0.03 84 2 123 "by doubleHit,freq,cluster" moderately radical 606050 6p21.3 ubiquitin D 397 rs8337 UBD 10537 6 29631655 NM_006398 NP_006389 C/G C160S minus 24341481 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.23 0.24 0.07 604 4 0.08 0.03 84 2 123 "by doubleHit,freq,cluster" moderately radical 606050 6p21.3 ubiquitin D 398 rs8337 UBD 10537 6 29631655 NM_006398 NP_006389 C/G C160S minus 24790044 1303 SEQUENOM CEPH CEPH (92) 184 0.28 0.24 0.07 604 4 0.08 0.03 84 2 123 "by doubleHit,freq,cluster" moderately radical 606050 6p21.3 ubiquitin D 399 rs8337 UBD 10537 6 29631655 NM_006398 NP_006389 C/G C160S minus 24796241 1303 SEQUENOM CEPH CEPH (92) 184 0.15 0.24 0.07 604 4 0.08 0.03 84 2 123 "by doubleHit,freq,cluster" moderately radical 606050 6p21.3 ubiquitin D 400 rs8455 LXN 56925 3 159871482 NM_020169 NP_064554 C/T H53R plus 14195380 1303 SEQUENOM CEPH CEPH (92) 92 0.45 0.42 0.07 140 2 0.23 0.06 94 2 123 by freq conservative 3q25.32 latexin 401 rs8455 LXN 56925 3 159871482 NM_020169 NP_064554 C/T H53R plus 24381862 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.35 0.42 0.07 140 2 0.23 0.06 94 2 123 by freq conservative 3q25.32 latexin 402 rs8473 MKI67 4288 10 129789568 NM_002417 NP_002408 A/G K3217E minus 10462 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.3 0.35 0.09 448 4 0.44 0.03 1588 3 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 176741 10q25-qter antigen identified by monoclonal antibody Ki-67 403 rs8473 MKI67 4288 10 129789568 NM_002417 NP_002408 A/G K3217E minus 10624698 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.47 0.35 0.09 448 4 0.44 0.03 1588 3 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 176741 10q25-qter antigen identified by monoclonal antibody Ki-67 404 rs8473 MKI67 4288 10 129789568 NM_002417 NP_002408 A/G K3217E minus 10624698 1303 SEQUENOM CEPH CEPH (92) 92 0.3 0.35 0.09 448 4 0.44 0.03 1588 3 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 176741 10q25-qter antigen identified by monoclonal antibody Ki-67 405 rs8473 MKI67 4288 10 129789568 NM_002417 NP_002408 A/G K3217E minus 23643988 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.38 0.35 0.09 448 4 0.44 0.03 1588 3 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 176741 10q25-qter antigen identified by monoclonal antibody Ki-67 406 rs8572 OXA1L 5018 14 22306364 NM_005015 NP_005006 A/G A104V minus 1487347 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 80 0.2 0.14 0.08 338 5 0.3 0.15 212 4 121 "by doubleHit,freq,cluster" Benign 0.173 8 moderately conservative 601066 14q11.2 oxidase (cytochrome c) assembly 1-like 407 rs8572 OXA1L 5018 14 22306364 NM_005015 NP_005006 A/G A104V minus 1487347 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.14 0.14 0.08 338 5 0.3 0.15 212 4 121 "by doubleHit,freq,cluster" Benign 0.173 8 moderately conservative 601066 14q11.2 oxidase (cytochrome c) assembly 1-like 408 rs8572 OXA1L 5018 14 22306364 NM_005015 NP_005006 A/G A104V minus 1487347 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 94 0.21 0.14 0.08 338 5 0.3 0.15 212 4 121 "by doubleHit,freq,cluster" Benign 0.173 8 moderately conservative 601066 14q11.2 oxidase (cytochrome c) assembly 1-like 409 rs8572 OXA1L 5018 14 22306364 NM_005015 NP_005006 A/G A104V minus 1487347 1303 SEQUENOM CEPH CEPH (92) 92 0.04 0.14 0.08 338 5 0.3 0.15 212 4 121 "by doubleHit,freq,cluster" Benign 0.173 8 moderately conservative 601066 14q11.2 oxidase (cytochrome c) assembly 1-like 410 rs8572 OXA1L 5018 14 22306364 NM_005015 NP_005006 A/G A104V minus 3173367 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 58 0.1 0.14 0.08 338 5 0.3 0.15 212 4 121 "by doubleHit,freq,cluster" Benign 0.173 8 moderately conservative 601066 14q11.2 oxidase (cytochrome c) assembly 1-like 411 rs8821 FLII 2314 17 18089259 NM_002018 NP_002009 A/G R1243H minus 10850 1303 SEQUENOM CEPH CEPH (92) 92 0.05 0.05 0 92 1 120 by freq Potentially damaging 1.308 8 Tolerant 0.54 2.76 78 conservative 600362 17p11.2 flightless I homolog (Drosophila) 412 rs8875 NDUFC2 4718 11 77468303 NM_004549 NP_004540 C/G L46V plus 793572 1303 SEQUENOM CEPH CEPH (92) 92 0.23 0.23 0 92 1 123 by freq Benign 0.761 6 conservative 603845 11q13.4 "NADH dehydrogenase (ubiquinone) 1, subcomplex unknown, 2, 14.5kDa" 413 rs8923 MTHFS 10588 15 77924615 NM_006441 NP_006432 A/G T202A minus 10798867 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.08 0.07 0.02 260 3 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 604197 15q24.3 "5,10-methenyltetrahydrofolate synthetase (5-formyltetrahydrofolate cyclo-ligase)" 414 rs8923 MTHFS 10588 15 77924615 NM_006441 NP_006432 A/G T202A minus 10798867 1303 SEQUENOM CEPH CEPH (92) 92 0.06 0.07 0.02 260 3 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 604197 15q24.3 "5,10-methenyltetrahydrofolate synthetase (5-formyltetrahydrofolate cyclo-ligase)" 415 rs8923 MTHFS 10588 15 77924615 NM_006441 NP_006432 A/G T202A minus 24521262 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.07 0.02 260 3 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 604197 15q24.3 "5,10-methenyltetrahydrofolate synthetase (5-formyltetrahydrofolate cyclo-ligase)" 416 rs8971 GART 2618 21 33805488 NM_000819 NP_000810 A/G D752G minus 11013 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.18 0.18 0 418 3 0.13 0.01 1576 3 123 "by cluster,freq" Possibly damaging 1.64 25 Tolerant 0.39 2.98 192 moderately conservative 138440 21q22.11 "phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole synthetase" 417 rs8971 GART 2618 21 33805488 NM_000819 NP_000810 A/G D752G minus 24546261 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.17 0.18 0 418 3 0.13 0.01 1576 3 123 "by cluster,freq" Possibly damaging 1.64 25 Tolerant 0.39 2.98 192 moderately conservative 138440 21q22.11 "phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole synthetase" 418 rs8971 GART 2618 21 33805488 NM_000819 NP_000810 A/G D752G minus 24796624 1303 SEQUENOM CEPH CEPH (92) 184 0.18 0.18 0 418 3 0.13 0.01 1576 3 123 "by cluster,freq" Possibly damaging 1.64 25 Tolerant 0.39 2.98 192 moderately conservative 138440 21q22.11 "phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole synthetase" 419 rs8999 TTF1 7270 9 132306895 NM_007344 NP_031370 G/T A290S minus 11043 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.08 0.07 0.01 212 2 0.26 0 1500 1 120 "HapMap,freq,cluster" moderately conservative 600777 9q34.3 "transcription termination factor, RNA polymerase I" 420 rs8999 TTF1 7270 9 132306895 NM_007344 NP_031370 G/T A290S minus 11043 1303 SEQUENOM CEPH CEPH (92) 92 0.06 0.07 0.01 212 2 0.26 0 1500 1 120 "HapMap,freq,cluster" moderately conservative 600777 9q34.3 "transcription termination factor, RNA polymerase I" 421 rs9002 GPR125 166647 4 22066436 XM_291111 XP_291111 A/G V1043M minus 6469754 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.27 0.16 0.18 212 2 123 "HapMap,doubleHit,freq" Borderline 0.17 2.78 34 conservative 4p15.32-p15.31 G protein-coupled receptor 125 422 rs9002 GPR125 166647 4 22066436 XM_291111 XP_291111 A/G V1043M minus 6469754 1303 SEQUENOM CEPH CEPH (92) 92 0.02 0.16 0.18 212 2 123 "HapMap,doubleHit,freq" Borderline 0.17 2.78 34 conservative 4p15.32-p15.31 G protein-coupled receptor 125 423 rs9250 SENP6 26054 6 76482008 NM_015571 NP_056386 A/G Y1106C plus 11320 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.25 0.3 0.06 522 5 0.02 0 44 1 123 "HapMap,doubleHit,submitter,freq,cluster" radical 605003 6q13-q14.3 SUMO1/sentrin specific protease 6 424 rs9250 SENP6 26054 6 76482008 NM_015571 NP_056386 A/G Y1106C plus 1517681 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 84 0.4 0.3 0.06 522 5 0.02 0 44 1 123 "HapMap,doubleHit,submitter,freq,cluster" radical 605003 6q13-q14.3 SUMO1/sentrin specific protease 6 425 rs9250 SENP6 26054 6 76482008 NM_015571 NP_056386 A/G Y1106C plus 11824656 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.34 0.3 0.06 522 5 0.02 0 44 1 123 "HapMap,doubleHit,submitter,freq,cluster" radical 605003 6q13-q14.3 SUMO1/sentrin specific protease 6 426 rs9250 SENP6 26054 6 76482008 NM_015571 NP_056386 A/G Y1106C plus 11824656 1303 SEQUENOM CEPH CEPH (92) 92 0.25 0.3 0.06 522 5 0.02 0 44 1 123 "HapMap,doubleHit,submitter,freq,cluster" radical 605003 6q13-q14.3 SUMO1/sentrin specific protease 6 427 rs9250 SENP6 26054 6 76482008 NM_015571 NP_056386 A/G Y1106C plus 24408636 1371 PERLEGEN AFD_EUR_PANEL European American (24) 38 0.32 0.3 0.06 522 5 0.02 0 44 1 123 "HapMap,doubleHit,submitter,freq,cluster" radical 605003 6q13-q14.3 SUMO1/sentrin specific protease 6 428 rs9436 PELP1 27043 17 4521500 NM_014389 NP_055204 A/T T1126S minus 11526 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.27 0.26 0.03 400 3 120 "HapMap,submitter,freq" moderately conservative 17p13.3 "proline-, glutamic acid-, leucine-rich protein 1" 429 rs9436 PELP1 27043 17 4521500 NM_014389 NP_055204 A/T T1126S minus 11526 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.22 0.26 0.03 400 3 120 "HapMap,submitter,freq" moderately conservative 17p13.3 "proline-, glutamic acid-, leucine-rich protein 1" 430 rs9436 PELP1 27043 17 4521500 NM_014389 NP_055204 A/T T1126S minus 11526 1303 SEQUENOM CEPH CEPH (92) 92 0.27 0.26 0.03 400 3 120 "HapMap,submitter,freq" moderately conservative 17p13.3 "proline-, glutamic acid-, leucine-rich protein 1" 431 rs9438 DHX36 170506 3 155501589 NM_020865 NP_065916 C/G S416C plus 11529 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.41 0.39 0.03 400 3 120 "HapMap,doubleHit,submitter,freq,cluster" Potentially damaging 1.437 6 moderately radical 3p13-q23 DEAH (Asp-Glu-Ala-His) box polypeptide 36 432 rs9438 DHX36 170506 3 155501589 NM_020865 NP_065916 C/G S416C plus 3110895 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.35 0.39 0.03 400 3 120 "HapMap,doubleHit,submitter,freq,cluster" Potentially damaging 1.437 6 moderately radical 3p13-q23 DEAH (Asp-Glu-Ala-His) box polypeptide 36 433 rs9438 DHX36 170506 3 155501589 NM_020865 NP_065916 C/G S416C plus 3110895 1303 SEQUENOM CEPH CEPH (92) 92 0.41 0.39 0.03 400 3 120 "HapMap,doubleHit,submitter,freq,cluster" Potentially damaging 1.437 6 moderately radical 3p13-q23 DEAH (Asp-Glu-Ala-His) box polypeptide 36 434 rs9508 ATPIF1 93974 1 28248421 NM_178190 NP_835497 C/T R63G minus 11605 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.23 0.22 0.02 328 3 0.24 0.23 94 2 123 "by doubleHit,submitter,freq" moderately radical 1p35.3 ATPase inhibitory factor 1 435 rs9508 ATPIF1 93974 1 28248421 NM_178190 NP_835497 C/T R63G minus 2287204 1303 SEQUENOM CEPH CEPH (92) 92 0.23 0.22 0.02 328 3 0.24 0.23 94 2 123 "by doubleHit,submitter,freq" moderately radical 1p35.3 ATPase inhibitory factor 1 436 rs9508 ATPIF1 93974 1 28248421 NM_178190 NP_835497 C/T R63G minus 23668319 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.19 0.22 0.02 328 3 0.24 0.23 94 2 123 "by doubleHit,submitter,freq" moderately radical 1p35.3 ATPase inhibitory factor 1 437 rs9600 NDUFS3 4722 11 47562560 NM_004551 NP_004542 A/C P249Q plus 11703 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 84 0.14 0.14 0 84 1 0.11 0 84 1 52 by freq Possibly damaging 1.872 14 Intolerant 0 3.17 19 moderately conservative 603846 11p11.11 "NADH dehydrogenase (ubiquinone) Fe-S protein 3, 30kDa (NADH-coenzyme Q reductase)" 438 rs9614 FBXO2 26232 1 11644827 NM_012168 NP_036300 A/C K118T minus 1343940 1303 SEQUENOM CEPH CEPH (92) 92 0.19 0.19 0 92 1 120 by freq Potentially damaging 1.363 11 Tolerant 0.23 2.81 33 moderately conservative 607112 1p36.21 F-box protein 2 439 rs10012 CYP1B1 1545 2 38214041 NM_000104 NP_000095 C/G R48G minus 6903740 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.23 0.3 0.13 326 3 0.34 0.04 346 4 123 "by doubleHit,freq,cluster" Benign 0.225 5 Tolerant 0.23 2.81 85 moderately radical 601771 2p21 "cytochrome P450, family 1, subfamily B, polypeptide 1" 440 rs10012 CYP1B1 1545 2 38214041 NM_000104 NP_000095 C/G R48G minus 12724380 693 EGP_SNPS PDR90 NIHPDR 172 0.4 0.3 0.13 326 3 0.34 0.04 346 4 123 "by doubleHit,freq,cluster" Benign 0.225 5 Tolerant 0.23 2.81 85 moderately radical 601771 2p21 "cytochrome P450, family 1, subfamily B, polypeptide 1" 441 rs10012 CYP1B1 1545 2 38214041 NM_000104 NP_000095 C/G R48G minus 12724380 1303 SEQUENOM CEPH CEPH (92) 92 0.16 0.3 0.13 326 3 0.34 0.04 346 4 123 "by doubleHit,freq,cluster" Benign 0.225 5 Tolerant 0.23 2.81 85 moderately radical 601771 2p21 "cytochrome P450, family 1, subfamily B, polypeptide 1" 442 rs10067 OVGP1 5016 1 111669353 NM_002557 NP_002548 C/G H604Q plus 12205 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 84 0.19 0.15 0.05 224 3 0.43 0.02 1542 5 123 "by submitter,freq,cluster" Probably damaging 2.063 6 conservative 603578 1p13 "oviductal glycoprotein 1, 120kDa (mucin 9, oviductin)" 443 rs10067 OVGP1 5016 1 111669353 NM_002557 NP_002548 C/G H604Q plus 2640019 1303 SEQUENOM CEPH CEPH (92) 92 0.1 0.15 0.05 224 3 0.43 0.02 1542 5 123 "by submitter,freq,cluster" Probably damaging 2.063 6 conservative 603578 1p13 "oviductal glycoprotein 1, 120kDa (mucin 9, oviductin)" 444 rs10067 OVGP1 5016 1 111669353 NM_002557 NP_002548 C/G H604Q plus 23860871 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.17 0.15 0.05 224 3 0.43 0.02 1542 5 123 "by submitter,freq,cluster" Probably damaging 2.063 6 conservative 603578 1p13 "oviductal glycoprotein 1, 120kDa (mucin 9, oviductin)" 445 rs10371 CACH-1 134526 5 80667398 NM_130767 NP_570123 C/T A403T plus 12523 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.2 0.2 0.01 520 4 120 "HapMap,submitter,freq,cluster" moderately conservative 5q14.1 cytosolic acetyl-CoA hydrolase 446 rs10371 CACH-1 134526 5 80667398 NM_130767 NP_570123 C/T A403T plus 1530425 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.21 0.2 0.01 520 4 120 "HapMap,submitter,freq,cluster" moderately conservative 5q14.1 cytosolic acetyl-CoA hydrolase 447 rs10371 CACH-1 134526 5 80667398 NM_130767 NP_570123 C/T A403T plus 17069119 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.21 0.2 0.01 520 4 120 "HapMap,submitter,freq,cluster" moderately conservative 5q14.1 cytosolic acetyl-CoA hydrolase 448 rs10371 CACH-1 134526 5 80667398 NM_130767 NP_570123 C/T A403T plus 17069119 1303 SEQUENOM CEPH CEPH (92) 92 0.2 0.2 0.01 520 4 120 "HapMap,submitter,freq,cluster" moderately conservative 5q14.1 cytosolic acetyl-CoA hydrolase 449 rs10502 UBE2J1 51465 6 90096389 NM_016021 NP_057105 C/G L229V minus 4963580 902 AFFY Caucasian 24 0.42 0.38 0.05 177 4 0.27 0.02 1636 6 123 by freq Benign 0.225 5 Tolerant 0.23 3.1 8 conservative 6q16.1 "ubiquitin-conjugating enzyme E2, J1 (UBC6 homolog, yeast)" 450 rs10502 UBE2J1 51465 6 90096389 NM_016021 NP_057105 C/G L229V minus 4963580 904 AFFY CEPH 12 0.33 0.38 0.05 177 4 0.27 0.02 1636 6 123 by freq Benign 0.225 5 Tolerant 0.23 3.1 8 conservative 6q16.1 "ubiquitin-conjugating enzyme E2, J1 (UBC6 homolog, yeast)" 451 rs10502 UBE2J1 51465 6 90096389 NM_016021 NP_057105 C/G L229V minus 12824947 1303 SEQUENOM CEPH CEPH (92) 93 0.41 0.38 0.05 177 4 0.27 0.02 1636 6 123 by freq Benign 0.225 5 Tolerant 0.23 3.1 8 conservative 6q16.1 "ubiquitin-conjugating enzyme E2, J1 (UBC6 homolog, yeast)" 452 rs10502 UBE2J1 51465 6 90096389 NM_016021 NP_057105 C/G L229V minus 24399052 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.31 0.38 0.05 177 4 0.27 0.02 1636 6 123 by freq Benign 0.225 5 Tolerant 0.23 3.1 8 conservative 6q16.1 "ubiquitin-conjugating enzyme E2, J1 (UBC6 homolog, yeast)" 453 rs10642 EIF5B 9669 2 99438715 NM_015904 NP_056988 A/G S337G plus 12805 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 84 0.03 0.03 0 84 1 0.09 0.05 168 2 52 by freq moderately conservative 606086 2p11.1-q11.1 eukaryotic translation initiation factor 5B 454 rs10963 RBP5 83758 12 7172584 NM_031491 NP_113679 C/T D19N plus 13141 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 84 0.23 0.23 0 84 1 0.4 0.03 1664 3 100 "by cluster,freq" Benign 0.338 26 Borderline 0.19 2.78 89 conservative 12p13.31 "retinol binding protein 5, cellular" 455 rs10988 LARS 51520 5 145480189 NM_020117 NP_064502 C/T R1088K plus 13168 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 84 0.17 0.25 0.06 532 5 0.21 0.05 1266 4 123 "HapMap,freq,cluster" Benign 0.984 13 conservative 151350 5q32 leucyl-tRNA synthetase 456 rs10988 LARS 51520 5 145480189 NM_020117 NP_064502 C/T R1088K plus 13168 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.24 0.25 0.06 532 5 0.21 0.05 1266 4 123 "HapMap,freq,cluster" Benign 0.984 13 conservative 151350 5q32 leucyl-tRNA synthetase 457 rs10988 LARS 51520 5 145480189 NM_020117 NP_064502 C/T R1088K plus 4949406 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.29 0.25 0.06 532 5 0.21 0.05 1266 4 123 "HapMap,freq,cluster" Benign 0.984 13 conservative 151350 5q32 leucyl-tRNA synthetase 458 rs10988 LARS 51520 5 145480189 NM_020117 NP_064502 C/T R1088K plus 4949406 1303 SEQUENOM CEPH CEPH (92) 92 0.24 0.25 0.06 532 5 0.21 0.05 1266 4 123 "HapMap,freq,cluster" Benign 0.984 13 conservative 151350 5q32 leucyl-tRNA synthetase 459 rs10988 LARS 51520 5 145480189 NM_020117 NP_064502 C/T R1088K plus 24351928 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.38 0.25 0.06 532 5 0.21 0.05 1266 4 123 "HapMap,freq,cluster" Benign 0.984 13 conservative 151350 5q32 leucyl-tRNA synthetase 460 rs11106 MKI67 4288 10 129789768 NM_002417 NP_002408 C/G T3150S minus 13291 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.43 0.43 0.01 364 3 0.47 0.03 126 2 121 "by doubleHit,freq,cluster" moderately conservative 176741 10q25-qter antigen identified by monoclonal antibody Ki-67 461 rs11106 MKI67 4288 10 129789768 NM_002417 NP_002408 C/G T3150S minus 1525715 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 84 0.45 0.43 0.01 364 3 0.47 0.03 126 2 121 "by doubleHit,freq,cluster" moderately conservative 176741 10q25-qter antigen identified by monoclonal antibody Ki-67 462 rs11106 MKI67 4288 10 129789768 NM_002417 NP_002408 C/G T3150S minus 10583404 1303 SEQUENOM CEPH CEPH (92) 92 0.42 0.43 0.01 364 3 0.47 0.03 126 2 121 "by doubleHit,freq,cluster" moderately conservative 176741 10q25-qter antigen identified by monoclonal antibody Ki-67 463 rs11159 RNASET2 8635 6 167313552 NM_003730 NP_003721 C/T R236W minus 13347 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.04 0.07 0.09 344 4 0.05 0.07 1754 5 123 "HapMap,freq,cluster" Benign 0.511 5 moderately radical 6q27 ribonuclease T2 464 rs11159 RNASET2 8635 6 167313552 NM_003730 NP_003721 C/T R236W minus 13347 1303 SEQUENOM CEPH CEPH (92) 92 0.01 0.07 0.09 344 4 0.05 0.07 1754 5 123 "HapMap,freq,cluster" Benign 0.511 5 moderately radical 6q27 ribonuclease T2 465 rs11159 RNASET2 8635 6 167313552 NM_003730 NP_003721 C/T R236W minus 1512972 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 84 0.21 0.07 0.09 344 4 0.05 0.07 1754 5 123 "HapMap,freq,cluster" Benign 0.511 5 moderately radical 6q27 ribonuclease T2 466 rs11159 RNASET2 8635 6 167313552 NM_003730 NP_003721 C/T R236W minus 24146236 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.07 0.09 344 4 0.05 0.07 1754 5 123 "HapMap,freq,cluster" Benign 0.511 5 moderately radical 6q27 ribonuclease T2 467 rs11250 CENPC1 1060 4 68208981 NM_001812 NP_001803 C/T L341F minus 5528842 1303 SEQUENOM CEPH CEPH (92) 92 0.35 0.35 0 92 1 121 "by doubleHit,freq,cluster" conservative 117141 4q12-q13.3 centromere protein C 1 468 rs11357 MTIF2 4528 2 55381766 NM_002453 NP_002444 A/G V556I minus 13561 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.15 0.2 0.13 240 2 121 "by doubleHit,freq,cluster" Benign 0.3 5 Tolerant 1 2.73 30 conservative 603766 2p14-p16 mitochondrial translational initiation factor 2 469 rs11357 MTIF2 4528 2 55381766 NM_002453 NP_002444 A/G V556I minus 3177497 619 WICVAR MITOGPOP6 CORIELL Mixed 52 0.37 0.2 0.13 240 2 121 "by doubleHit,freq,cluster" Benign 0.3 5 Tolerant 1 2.73 30 conservative 603766 2p14-p16 mitochondrial translational initiation factor 2 470 rs11479 ECGF1 1890 22 49254380 NM_001953 NP_001944 C/T S471L minus 13689 1303 SEQUENOM CEPH CEPH (92) 92 0.05 0.05 0 92 1 123 "by cluster,freq" Tolerant 0.46 2.92 57 moderately radical 131222 22q13.33 endothelial cell growth factor 1 (platelet-derived) 471 rs11551 FBLN1 2192 22 44279529 NM_001996 NP_001987 G/T R633L plus 13769 1303 SEQUENOM CEPH CEPH (92) 92 0.12 0.12 0 92 1 120 by freq Potentially damaging 1.278 14 Tolerant 1 2.77 19 moderately radical 135820 22q13.31 fibulin 1 472 rs11574 ID3 3399 1 23630804 NM_002167 NP_002158 A/G T105A minus 13793 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.2 0.23 0.06 308 2 121 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 600277 1p36.13-p36.12 "inhibitor of DNA binding 3, dominant negative helix-loop-helix protein" 473 rs11574 ID3 3399 1 23630804 NM_002167 NP_002158 A/G T105A minus 3069953 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.28 0.23 0.06 308 2 121 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 600277 1p36.13-p36.12 "inhibitor of DNA binding 3, dominant negative helix-loop-helix protein" 474 rs11607 MBTPS1 8720 16 82645548 NM_201268 NP_957720 A/G S627N minus 13830 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.39 0.36 0.06 306 2 0.42 0 1120 1 121 "HapMap,doubleHit,freq,cluster" conservative 603355 16q24 "membrane-bound transcription factor protease, site 1" 475 rs11607 MBTPS1 8720 16 82645548 NM_201268 NP_957720 A/G S627N minus 19343224 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.31 0.36 0.06 306 2 0.42 0 1120 1 121 "HapMap,doubleHit,freq,cluster" conservative 603355 16q24 "membrane-bound transcription factor protease, site 1" 476 rs11746 FREB 84824 1 158414794 NM_032738 NP_116127 A/G R349Q plus 13980 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.44 0.44 0.01 328 3 0.23 0.04 94 2 123 "by doubleHit,freq,cluster" conservative 606891 1q23.1 Fc receptor homolog expressed in B cells 477 rs11746 FREB 84824 1 158414794 NM_032738 NP_116127 A/G R349Q plus 1291097 1303 SEQUENOM CEPH CEPH (92) 92 0.44 0.44 0.01 328 3 0.23 0.04 94 2 123 "by doubleHit,freq,cluster" conservative 606891 1q23.1 Fc receptor homolog expressed in B cells 478 rs11746 FREB 84824 1 158414794 NM_032738 NP_116127 A/G R349Q plus 24244157 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.46 0.44 0.01 328 3 0.23 0.04 94 2 123 "by doubleHit,freq,cluster" conservative 606891 1q23.1 Fc receptor homolog expressed in B cells 479 rs12505 CKB 1152 14 103056022 NM_001823 NP_001814 C/T L360F minus 24796478 1303 SEQUENOM CEPH CEPH (92) 184 0.41 0.41 0 184 1 123 by freq Possibly damaging 1.696 116 Intolerant 0 2.79 153 conservative 123280 14q32 "creatine kinase, brain" 480 rs12529 AKR1C3 8644 10 5126651 NM_003739 NP_003730 C/G H5Q plus 14808 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.4 0.41 0.04 385 4 0.17 0.15 1996 7 121 "by doubleHit,freq,cluster" Benign 0.483 76 Tolerant 0.31 2.88 68 conservative 603966 10p15-p14 "aldo-keto reductase family 1, member C3 (3-alpha hydroxysteroid dehydrogenase, type II)" 481 rs12529 AKR1C3 8644 10 5126651 NM_003739 NP_003730 C/G H5Q plus 2827711 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 42 0.5 0.41 0.04 385 4 0.17 0.15 1996 7 121 "by doubleHit,freq,cluster" Benign 0.483 76 Tolerant 0.31 2.88 68 conservative 603966 10p15-p14 "aldo-keto reductase family 1, member C3 (3-alpha hydroxysteroid dehydrogenase, type II)" 482 rs12529 AKR1C3 8644 10 5126651 NM_003739 NP_003730 C/G H5Q plus 2827711 1303 SEQUENOM CEPH CEPH (92) 93 0.4 0.41 0.04 385 4 0.17 0.15 1996 7 121 "by doubleHit,freq,cluster" Benign 0.483 76 Tolerant 0.31 2.88 68 conservative 603966 10p15-p14 "aldo-keto reductase family 1, member C3 (3-alpha hydroxysteroid dehydrogenase, type II)" 483 rs12529 AKR1C3 8644 10 5126651 NM_003739 NP_003730 C/G H5Q plus 6903636 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.39 0.41 0.04 385 4 0.17 0.15 1996 7 121 "by doubleHit,freq,cluster" Benign 0.483 76 Tolerant 0.31 2.88 68 conservative 603966 10p15-p14 "aldo-keto reductase family 1, member C3 (3-alpha hydroxysteroid dehydrogenase, type II)" 484 rs12614 BF 629 6 32022158 NM_001710 NP_001701 C/T R32W plus 5606985 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 28 0.07 0.08 0.01 74 2 0.17 0 96 2 123 by freq moderately radical 138470 6p21.3 "B-factor, properdin" 485 rs12614 BF 629 6 32022158 NM_001710 NP_001701 C/T R32W plus 12674482 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.09 0.08 0.01 74 2 0.17 0 96 2 123 by freq moderately radical 138470 6p21.3 "B-factor, properdin" 486 rs12770 RANBP2 5903 2 108841187 NM_006267 NP_006258 C/G P1892A minus 15067 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.22 0.22 0 188 1 108 by freq conservative 601181 2q12.3 RAN binding protein 2 487 rs12917 MGMT 4255 10 131396273 NM_002412 NP_002403 C/T L84F plus 15222 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.25 0.18 0.04 1108 4 0.12 0.02 1902 7 123 "by cluster,freq" Benign 0.463 7 Tolerant 0.71 2.9 15 conservative 156569 10q26 O-6-methylguanine-DNA methyltransferase 488 rs12917 MGMT 4255 10 131396273 NM_002412 NP_002403 C/T L84F plus 2924003 506 NCBI NIHPDR NIHPDR 810 0.18 0.18 0.04 1108 4 0.12 0.02 1902 7 123 "by cluster,freq" Benign 0.463 7 Tolerant 0.71 2.9 15 conservative 156569 10q26 O-6-methylguanine-DNA methyltransferase 489 rs12917 MGMT 4255 10 131396273 NM_002412 NP_002403 C/T L84F plus 5586758 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.11 0.18 0.04 1108 4 0.12 0.02 1902 7 123 "by cluster,freq" Benign 0.463 7 Tolerant 0.71 2.9 15 conservative 156569 10q26 O-6-methylguanine-DNA methyltransferase 490 rs12917 MGMT 4255 10 131396273 NM_002412 NP_002403 C/T L84F plus 23564520 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.18 0.04 1108 4 0.12 0.02 1902 7 123 "by cluster,freq" Benign 0.463 7 Tolerant 0.71 2.9 15 conservative 156569 10q26 O-6-methylguanine-DNA methyltransferase 491 rs12960 SPG7 6687 16 88147829 NM_003119 NP_003110 A/G R688Q plus 75236 1303 SEQUENOM CEPH CEPH (92) 92 0.14 0.14 0.01 140 2 0.11 0.08 130 4 123 "by doubleHit,submitter,freq,cluster" Potentially damaging 1.357 9 Tolerant 0.41 2.75 61 conservative 602783 16q24.3 "spastic paraplegia 7, paraplegin (pure and complicated autosomal recessive)" 492 rs12960 SPG7 6687 16 88147829 NM_003119 NP_003110 A/G R688Q plus 24096097 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.14 0.01 140 2 0.11 0.08 130 4 123 "by doubleHit,submitter,freq,cluster" Potentially damaging 1.357 9 Tolerant 0.41 2.75 61 conservative 602783 16q24.3 "spastic paraplegia 7, paraplegin (pure and complicated autosomal recessive)" 493 rs13021 PNN 5411 14 38720675 NM_002687 NP_002678 A/G S671G plus 15334 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.12 0.1 0.03 448 4 0.2 0.13 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 603154 14q13.3 "pinin, desmosome associated protein" 494 rs13021 PNN 5411 14 38720675 NM_002687 NP_002678 A/G S671G plus 15334 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.08 0.1 0.03 448 4 0.2 0.13 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 603154 14q13.3 "pinin, desmosome associated protein" 495 rs13021 PNN 5411 14 38720675 NM_002687 NP_002678 A/G S671G plus 14373749 1303 SEQUENOM CEPH CEPH (92) 92 0.12 0.1 0.03 448 4 0.2 0.13 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 603154 14q13.3 "pinin, desmosome associated protein" 496 rs13021 PNN 5411 14 38720675 NM_002687 NP_002678 A/G S671G plus 24112453 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.1 0.03 448 4 0.2 0.13 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 603154 14q13.3 "pinin, desmosome associated protein" 497 rs13090 THRAP5 10025 19 819115 NM_005481 NP_005472 A/G E874K minus 15405 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.26 0.25 0.01 400 3 120 "HapMap,doubleHit,freq" moderately conservative 604062 19p13.3 thyroid hormone receptor associated protein 5 498 rs13090 THRAP5 10025 19 819115 NM_005481 NP_005472 A/G E874K minus 2513099 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.24 0.25 0.01 400 3 120 "HapMap,doubleHit,freq" moderately conservative 604062 19p13.3 thyroid hormone receptor associated protein 5 499 rs13090 THRAP5 10025 19 819115 NM_005481 NP_005472 A/G E874K minus 2513099 1303 SEQUENOM CEPH CEPH (92) 92 0.26 0.25 0.01 400 3 120 "HapMap,doubleHit,freq" moderately conservative 604062 19p13.3 thyroid hormone receptor associated protein 5 500 rs13181 ERCC2 2068 19 50546759 NM_000400 NP_000391 G/T K751Q plus 4385756 693 EGP_SNPS PDR90 NIHPDR 162 0.22 0.24 0.08 364 4 0.18 0.09 436 6 123 "by doubleHit,freq" Benign 0.472 5 Tolerant 0.7 3.14 28 moderately conservative 126340 19q13.3 "excision repair cross-complementing rodent repair deficiency, complementation group 2 (xeroderma pigmentosum D)" 501 rs13181 ERCC2 2068 19 50546759 NM_000400 NP_000391 G/T K751Q plus 4385756 1303 SEQUENOM CEPH CEPH (92) 92 0.19 0.24 0.08 364 4 0.18 0.09 436 6 123 "by doubleHit,freq" Benign 0.472 5 Tolerant 0.7 3.14 28 moderately conservative 126340 19q13.3 "excision repair cross-complementing rodent repair deficiency, complementation group 2 (xeroderma pigmentosum D)" 502 rs13181 ERCC2 2068 19 50546759 NM_000400 NP_000391 G/T K751Q plus 5586504 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.27 0.24 0.08 364 4 0.18 0.09 436 6 123 "by doubleHit,freq" Benign 0.472 5 Tolerant 0.7 3.14 28 moderately conservative 126340 19q13.3 "excision repair cross-complementing rodent repair deficiency, complementation group 2 (xeroderma pigmentosum D)" 503 rs13181 ERCC2 2068 19 50546759 NM_000400 NP_000391 G/T K751Q plus 24431306 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.4 0.24 0.08 364 4 0.18 0.09 436 6 123 "by doubleHit,freq" Benign 0.472 5 Tolerant 0.7 3.14 28 moderately conservative 126340 19q13.3 "excision repair cross-complementing rodent repair deficiency, complementation group 2 (xeroderma pigmentosum D)" 504 rs13321 TNC 3371 9 114872137 NM_002160 NP_002151 C/G E2008Q minus 15647 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.33 0.32 0.02 400 3 0.45 0 1502 1 121 "HapMap,doubleHit,submitter,freq,cluster" conservative 187380 9q33 tenascin C (hexabrachion) 505 rs13321 TNC 3371 9 114872137 NM_002160 NP_002151 C/G E2008Q minus 15647 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.29 0.32 0.02 400 3 0.45 0 1502 1 121 "HapMap,doubleHit,submitter,freq,cluster" conservative 187380 9q33 tenascin C (hexabrachion) 506 rs13321 TNC 3371 9 114872137 NM_002160 NP_002151 C/G E2008Q minus 17996538 1303 SEQUENOM CEPH CEPH (92) 92 0.33 0.32 0.02 400 3 0.45 0 1502 1 121 "HapMap,doubleHit,submitter,freq,cluster" conservative 187380 9q33 tenascin C (hexabrachion) 507 rs13428 ADPRTL1 143 13 23907441 NM_006437 NP_006428 C/G G1280R minus 15756 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.38 0.4 0.04 342 3 0.32 0.07 1832 5 123 "by doubleHit,freq,cluster" moderately radical 607519 13q11 ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1 508 rs13428 ADPRTL1 143 13 23907441 NM_006437 NP_006428 C/G G1280R minus 5586208 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.47 0.4 0.04 342 3 0.32 0.07 1832 5 123 "by doubleHit,freq,cluster" moderately radical 607519 13q11 ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1 509 rs13428 ADPRTL1 143 13 23907441 NM_006437 NP_006428 C/G G1280R minus 5586208 1303 SEQUENOM CEPH CEPH (92) 92 0.38 0.4 0.04 342 3 0.32 0.07 1832 5 123 "by doubleHit,freq,cluster" moderately radical 607519 13q11 ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1 510 rs13706 CDC6 990 17 35710677 NM_001254 NP_001245 A/G V441I plus 3177778 619 WICVAR MITOGPOP6 CORIELL Mixed 42 0.29 0.15 0.08 474 5 0.44 0.01 1580 3 123 "HapMap,freq,cluster" Benign 0.62 11 Intolerant 0.05 2.86 15 conservative 602627 17q21.3 CDC6 cell division cycle 6 homolog (S. cerevisiae) 511 rs13706 CDC6 990 17 35710677 NM_001254 NP_001245 A/G V441I plus 5587265 693 EGP_SNPS PDR90 NIHPDR 176 0.2 0.15 0.08 474 5 0.44 0.01 1580 3 123 "HapMap,freq,cluster" Benign 0.62 11 Intolerant 0.05 2.86 15 conservative 602627 17q21.3 CDC6 cell division cycle 6 homolog (S. cerevisiae) 512 rs13706 CDC6 990 17 35710677 NM_001254 NP_001245 A/G V441I plus 5587265 885 TSC-CSHL HapMap-CEPH-30-trios 116 0.15 0.15 0.08 474 5 0.44 0.01 1580 3 123 "HapMap,freq,cluster" Benign 0.62 11 Intolerant 0.05 2.86 15 conservative 602627 17q21.3 CDC6 cell division cycle 6 homolog (S. cerevisiae) 513 rs13706 CDC6 990 17 35710677 NM_001254 NP_001245 A/G V441I plus 5587265 1303 SEQUENOM CEPH CEPH (92) 92 0.04 0.15 0.08 474 5 0.44 0.01 1580 3 123 "HapMap,freq,cluster" Benign 0.62 11 Intolerant 0.05 2.86 15 conservative 602627 17q21.3 CDC6 cell division cycle 6 homolog (S. cerevisiae) 514 rs13706 CDC6 990 17 35710677 NM_001254 NP_001245 A/G V441I plus 23618880 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.15 0.08 474 5 0.44 0.01 1580 3 123 "HapMap,freq,cluster" Benign 0.62 11 Intolerant 0.05 2.86 15 conservative 602627 17q21.3 CDC6 cell division cycle 6 homolog (S. cerevisiae) 515 rs13807 FAU 2197 11 64645610 NM_001997 NP_001988 C/T T53I minus 870143 555 UUGC NIH90 NIHPDR 180 0.01 0.01 0 360 2 120 "by cluster,freq" Potentially damaging 1.387 22 Intolerant 0 3.11 399 moderately conservative 134690 11q13 Finkel-Biskis-Reilly murine sarcoma virus (FBR-MuSV) ubiquitously expressed (fox derived); ribosomal protein S30 516 rs13807 FAU 2197 11 64645610 NM_001997 NP_001988 C/T T53I minus 12709616 693 EGP_SNPS PDR90 NIHPDR 180 0.01 0.01 0 360 2 120 "by cluster,freq" Potentially damaging 1.387 22 Intolerant 0 3.11 399 moderately conservative 134690 11q13 Finkel-Biskis-Reilly murine sarcoma virus (FBR-MuSV) ubiquitously expressed (fox derived); ribosomal protein S30 517 rs13817 MUS81 80198 11 65384910 NM_025128 NP_079404 A/G R37H plus 16171 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.2 0.2 0 280 2 121 "by doubleHit,freq,cluster" conservative 606591 11q13 MUS81 endonuclease homolog (yeast) 518 rs13817 MUS81 80198 11 65384910 NM_025128 NP_079404 A/G R37H plus 1727380 1303 SEQUENOM CEPH CEPH (92) 92 0.2 0.2 0 280 2 121 "by doubleHit,freq,cluster" conservative 606591 11q13 MUS81 endonuclease homolog (yeast) 519 rs13894 SAT2 112483 17 7470627 NM_133491 NP_597998 C/T R126C minus 14295724 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.1 0.07 0.04 212 2 0.06 0 1476 1 120 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.987 5 Intolerant 0.02 2.76 32 radical 17p13.2 spermidine/spermine N1-acetyltransferase 2 520 rs13894 SAT2 112483 17 7470627 NM_133491 NP_597998 C/T R126C minus 14295724 1303 SEQUENOM CEPH CEPH (92) 92 0.04 0.07 0.04 212 2 0.06 0 1476 1 120 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.987 5 Intolerant 0.02 2.76 32 radical 17p13.2 spermidine/spermine N1-acetyltransferase 2 521 rs13898 AEBP1 165 7 43927065 NM_001129 NP_001120 A/G V1148I plus 4479021 693 EGP_SNPS PDR90 NIHPDR 170 0.01 0.03 0.04 382 3 121 "HapMap,freq,cluster" Benign 0.225 8 conservative 602981 7p13 AE binding protein 1 522 rs13898 AEBP1 165 7 43927065 NM_001129 NP_001120 A/G V1148I plus 4479021 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.08 0.03 0.04 382 3 121 "HapMap,freq,cluster" Benign 0.225 8 conservative 602981 7p13 AE binding protein 1 523 rs13898 AEBP1 165 7 43927065 NM_001129 NP_001120 A/G V1148I plus 4479021 1303 SEQUENOM CEPH CEPH (92) 92 0.02 0.03 0.04 382 3 121 "HapMap,freq,cluster" Benign 0.225 8 conservative 602981 7p13 AE binding protein 1 524 rs13926 TRAP1 10131 16 3664466 NM_016292 NP_057376 C/G R307G minus 89200 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.49 0.47 0.02 258 3 0.42 0.06 1484 3 123 "HapMap,doubleHit,freq,cluster" Benign 0.189 11 moderately radical 606219 16p13.3 heat shock protein 75 525 rs13926 TRAP1 10131 16 3664466 NM_016292 NP_057376 C/G R307G minus 89200 1303 SEQUENOM CEPH CEPH (92) 92 0.46 0.47 0.02 258 3 0.42 0.06 1484 3 123 "HapMap,doubleHit,freq,cluster" Benign 0.189 11 moderately radical 606219 16p13.3 heat shock protein 75 526 rs13926 TRAP1 10131 16 3664466 NM_016292 NP_057376 C/G R307G minus 24217057 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.46 0.47 0.02 258 3 0.42 0.06 1484 3 123 "HapMap,doubleHit,freq,cluster" Benign 0.189 11 moderately radical 606219 16p13.3 heat shock protein 75 527 rs13928 AEBP1 165 7 43927020 NM_001129 NP_001120 A/G K1133E plus 3177826 619 WICVAR MITOGPOP6 CORIELL Mixed 44 0.45 0.44 0.01 136 2 121 "by doubleHit,freq,cluster" Benign 0.007 8 moderately conservative 602981 7p13 AE binding protein 1 528 rs13928 AEBP1 165 7 43927020 NM_001129 NP_001120 A/G K1133E plus 3177826 1303 SEQUENOM CEPH CEPH (92) 92 0.44 0.44 0.01 136 2 121 "by doubleHit,freq,cluster" Benign 0.007 8 moderately conservative 602981 7p13 AE binding protein 1 529 rs14008 TACSTD2 4070 1 58754202 NM_002353 NP_002344 A/C D216E minus 650638 1303 SEQUENOM CEPH CEPH (92) 92 0.01 0.04 0.03 276 2 0.11 0 1470 1 123 "by doubleHit,freq,cluster" conservative 137290 1p32-p31 tumor-associated calcium signal transducer 2 530 rs14008 TACSTD2 4070 1 58754202 NM_002353 NP_002344 A/C D216E minus 24796670 1303 SEQUENOM CEPH CEPH (92) 184 0.05 0.04 0.03 276 2 0.11 0 1470 1 123 "by doubleHit,freq,cluster" conservative 137290 1p32-p31 tumor-associated calcium signal transducer 2 531 rs14024 KRT1 3848 12 51355281 NM_006121 NP_006112 A/G K633R minus 16388 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.42 0.4 0.04 446 4 0.36 0.06 1592 3 123 "HapMap,doubleHit,freq,cluster" conservative 139350 12q12-q13 keratin 1 (epidermolytic hyperkeratosis) 532 rs14024 KRT1 3848 12 51355281 NM_006121 NP_006112 A/G K633R minus 3869018 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.34 0.4 0.04 446 4 0.36 0.06 1592 3 123 "HapMap,doubleHit,freq,cluster" conservative 139350 12q12-q13 keratin 1 (epidermolytic hyperkeratosis) 533 rs14024 KRT1 3848 12 51355281 NM_006121 NP_006112 A/G K633R minus 16565519 1303 SEQUENOM CEPH CEPH (92) 92 0.42 0.4 0.04 446 4 0.36 0.06 1592 3 123 "HapMap,doubleHit,freq,cluster" conservative 139350 12q12-q13 keratin 1 (epidermolytic hyperkeratosis) 534 rs14024 KRT1 3848 12 51355281 NM_006121 NP_006112 A/G K633R minus 23957083 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.4 0.4 0.04 446 4 0.36 0.06 1592 3 123 "HapMap,doubleHit,freq,cluster" conservative 139350 12q12-q13 keratin 1 (epidermolytic hyperkeratosis) 535 rs14115 HSPC051 29796 22 28488080 NM_013387 NP_037519 A/G I47V plus 3226471 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.03 0.03 0.01 168 2 0.06 0.06 1590 3 123 "HapMap,submitter,freq,cluster" Benign 0.959 9 Tolerant 0.75 2.98 19 conservative 22cen-q12.3 ubiquinol-cytochrome c reductase complex (7.2 kD) 536 rs14115 HSPC051 29796 22 28488080 NM_013387 NP_037519 A/G I47V plus 23592348 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.03 0.01 168 2 0.06 0.06 1590 3 123 "HapMap,submitter,freq,cluster" Benign 0.959 9 Tolerant 0.75 2.98 19 conservative 22cen-q12.3 ubiquinol-cytochrome c reductase complex (7.2 kD) 537 rs15895 OAS2 4939 12 111911008 NM_016817 NP_058197 C/T STOP720W minus 18316 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.33 0.37 0.05 526 5 0.12 0.05 70 2 123 "by doubleHit,submitter,freq,cluster" Probably damaging Intolerant radical 603350 12q24.2 "2'-5'-oligoadenylate synthetase 2, 69/71kDa" 538 rs15895 OAS2 4939 12 111911008 NM_016817 NP_058197 C/T STOP720W minus 2055335 1303 SEQUENOM CEPH CEPH (92) 92 0.33 0.37 0.05 526 5 0.12 0.05 70 2 123 "by doubleHit,submitter,freq,cluster" Probably damaging Intolerant radical 603350 12q24.2 "2'-5'-oligoadenylate synthetase 2, 69/71kDa" 539 rs15895 OAS2 4939 12 111911008 NM_016817 NP_058197 C/T STOP720W minus 2428576 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.43 0.37 0.05 526 5 0.12 0.05 70 2 123 "by doubleHit,submitter,freq,cluster" Probably damaging Intolerant radical 603350 12q24.2 "2'-5'-oligoadenylate synthetase 2, 69/71kDa" 540 rs15895 OAS2 4939 12 111911008 NM_016817 NP_058197 C/T STOP720W minus 2428576 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 184 0.41 0.37 0.05 526 5 0.12 0.05 70 2 123 "by doubleHit,submitter,freq,cluster" Probably damaging Intolerant radical 603350 12q24.2 "2'-5'-oligoadenylate synthetase 2, 69/71kDa" 541 rs15895 OAS2 4939 12 111911008 NM_016817 NP_058197 C/T STOP720W minus 24416187 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.44 0.37 0.05 526 5 0.12 0.05 70 2 123 "by doubleHit,submitter,freq,cluster" Probably damaging Intolerant radical 603350 12q24.2 "2'-5'-oligoadenylate synthetase 2, 69/71kDa" 542 rs15911 CTBS 1486 1 84741098 NM_004388 NP_004379 C/T V274I plus 4391078 1303 SEQUENOM CEPH CEPH (92) 92 0.48 0.45 0.07 140 2 0.07 0.05 94 2 123 by freq Benign 0.835 6 Tolerant 0.41 2.86 11 conservative 600873 1p22 "chitobiase, di-N-acetyl-" 543 rs15911 CTBS 1486 1 84741098 NM_004388 NP_004379 C/T V274I plus 24238464 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.38 0.45 0.07 140 2 0.07 0.05 94 2 123 by freq Benign 0.835 6 Tolerant 0.41 2.86 11 conservative 600873 1p22 "chitobiase, di-N-acetyl-" 544 rs15922 TAF11 6882 6 34958804 NM_005643 NP_005634 C/G T68R minus 6312498 693 EGP_SNPS PDR90 NIHPDR 180 0.02 0.03 0.02 320 3 123 "by cluster,freq" Benign 0.13 14 Tolerant 0.52 3 11 moderately conservative 600772 6p21.31 "TAF11 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 28kDa" 545 rs15922 TAF11 6882 6 34958804 NM_005643 NP_005634 C/G T68R minus 6312498 1303 SEQUENOM CEPH CEPH (92) 92 0.03 0.03 0.02 320 3 123 "by cluster,freq" Benign 0.13 14 Tolerant 0.52 3 11 moderately conservative 600772 6p21.31 "TAF11 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 28kDa" 546 rs15922 TAF11 6882 6 34958804 NM_005643 NP_005634 C/G T68R minus 24383722 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.03 0.02 320 3 123 "by cluster,freq" Benign 0.13 14 Tolerant 0.52 3 11 moderately conservative 600772 6p21.31 "TAF11 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 28kDa" 547 rs17456 FDPS 2224 1 152103384 NM_002004 NP_001995 C/T I391V minus 20086 1303 SEQUENOM CEPH CEPH (92) 92 0.04 0.04 0 92 1 60 by freq Benign 0.148 16 Borderline 0.16 2.77 75 conservative 134629 1q22 "farnesyl diphosphate synthase (farnesyl pyrophosphate synthetase, dimethylallyltranstransferase, geranyltranstransferase)" 548 rs17560 ANG 283 14 20231813 NM_001145 NP_001136 A/G K84E plus 20171 523 WIAF-CSNP WIAF-CSNP-MITOGPOP4 "Europeans (20), Asians (10) and African-Americans (10)" 40 0.1 0.1 0 40 1 0.04 0 46 1 123 by freq Benign 0.019 31 Tolerant 0.78 2.89 173 moderately conservative 105850 14q11.1-q11.2 "angiogenin, ribonuclease, RNase A family, 5" 549 rs17561 IL1A 3552 2 113253454 NM_000575 NP_000566 G/T A114S minus 20172 523 WIAF-CSNP WIAF-CSNP-MITOGPOP4 "Europeans (20), Asians (10) and African-Americans (10)" 40 0.33 0.37 0.08 360 5 0.22 0.03 394 5 113 "HapMap,submitter,freq,cluster" Potentially damaging 1.296 24 Intolerant 0.03 2.8 33 moderately conservative 147760 2q14 "interleukin 1, alpha" 550 rs17561 IL1A 3552 2 113253454 NM_000575 NP_000566 G/T A114S minus 4969895 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.33 0.37 0.08 360 5 0.22 0.03 394 5 113 "HapMap,submitter,freq,cluster" Potentially damaging 1.296 24 Intolerant 0.03 2.8 33 moderately conservative 147760 2q14 "interleukin 1, alpha" 551 rs17561 IL1A 3552 2 113253454 NM_000575 NP_000566 G/T A114S minus 4969895 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.31 0.37 0.08 360 5 0.22 0.03 394 5 113 "HapMap,submitter,freq,cluster" Potentially damaging 1.296 24 Intolerant 0.03 2.8 33 moderately conservative 147760 2q14 "interleukin 1, alpha" 552 rs17561 IL1A 3552 2 113253454 NM_000575 NP_000566 G/T A114S minus 4969895 1303 SEQUENOM CEPH CEPH (92) 92 0.48 0.37 0.08 360 5 0.22 0.03 394 5 113 "HapMap,submitter,freq,cluster" Potentially damaging 1.296 24 Intolerant 0.03 2.8 33 moderately conservative 147760 2q14 "interleukin 1, alpha" 553 rs17561 IL1A 3552 2 113253454 NM_000575 NP_000566 G/T A114S minus 5586646 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.36 0.37 0.08 360 5 0.22 0.03 394 5 113 "HapMap,submitter,freq,cluster" Potentially damaging 1.296 24 Intolerant 0.03 2.8 33 moderately conservative 147760 2q14 "interleukin 1, alpha" 554 rs17562 IL1A 3552 2 113253421 NM_000575 NP_000566 A/G N125D minus 20173 523 WIAF-CSNP WIAF-CSNP-MITOGPOP4 "Europeans (20), Asians (10) and African-Americans (10)" 40 0.03 0.03 0 40 1 0.02 0.03 252 2 113 "by cluster,freq" Possibly damaging 1.691 25 Tolerant 0.27 2.91 31 conservative 147760 2q14 "interleukin 1, alpha" 555 rs17567 EPS15 2060 1 51538942 NM_001981 NP_001972 C/T I822M plus 20178 523 WIAF-CSNP WIAF-CSNP-MITOGPOP4 "Europeans (20), Asians (10) and African-Americans (10)" 40 0.33 0.22 0.1 132 2 123 "by doubleHit,freq,cluster" Tolerant 0.22 3 12 conservative 600051 1p32 epidermal growth factor receptor pathway substrate 15 556 rs17567 EPS15 2060 1 51538942 NM_001981 NP_001972 C/T I822M plus 2755092 1303 SEQUENOM CEPH CEPH (92) 92 0.17 0.22 0.1 132 2 123 "by doubleHit,freq,cluster" Tolerant 0.22 3 12 conservative 600051 1p32 epidermal growth factor receptor pathway substrate 15 557 rs17571 CTSD 1509 11 1739170 NM_001909 NP_001900 C/T A58V minus 20182 523 WIAF-CSNP WIAF-CSNP-MITOGPOP4 "Europeans (20), Asians (10) and African-Americans (10)" 40 0.1 0.08 0.01 252 3 63 "HapMap,freq" Benign 0.03 33 Tolerant 0.52 2.85 51 moderately conservative 116840 11p15.5 cathepsin D (lysosomal aspartyl protease) 558 rs17571 CTSD 1509 11 1739170 NM_001909 NP_001900 C/T A58V minus 20182 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.07 0.08 0.01 252 3 63 "HapMap,freq" Benign 0.03 33 Tolerant 0.52 2.85 51 moderately conservative 116840 11p15.5 cathepsin D (lysosomal aspartyl protease) 559 rs17571 CTSD 1509 11 1739170 NM_001909 NP_001900 C/T A58V minus 20182 1303 SEQUENOM CEPH CEPH (92) 92 0.08 0.08 0.01 252 3 63 "HapMap,freq" Benign 0.03 33 Tolerant 0.52 2.85 51 moderately conservative 116840 11p15.5 cathepsin D (lysosomal aspartyl protease) 560 rs17580 SERPINA1 5265 14 93917015 NM_000295 NP_000286 A/T E288V minus 20191 523 WIAF-CSNP WIAF-CSNP-MITOGPOP4 "Europeans (20), Asians (10) and African-Americans (10)" 38 0.03 0.07 0.03 130 2 123 by freq Intolerant 0 2.75 79 moderately radical 107400 14q32.1 "serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1" 561 rs17580 SERPINA1 5265 14 93917015 NM_000295 NP_000286 A/T E288V minus 3881969 1303 SEQUENOM CEPH CEPH (92) 92 0.08 0.07 0.03 130 2 123 by freq Intolerant 0 2.75 79 moderately radical 107400 14q32.1 "serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1" 562 rs17607 CD68 968 17 7425506 NM_001251 NP_001242 A/G A340T plus 20219 523 WIAF-CSNP WIAF-CSNP-MITOGPOP4 "Europeans (20), Asians (10) and African-Americans (10)" 38 0.03 0.06 0.01 250 3 63 "HapMap,freq" Benign 0.227 7 Tolerant 0.52 2.76 24 moderately conservative 153634 17p13 CD68 antigen 563 rs17607 CD68 968 17 7425506 NM_001251 NP_001242 A/G A340T plus 20219 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.06 0.06 0.01 250 3 63 "HapMap,freq" Benign 0.227 7 Tolerant 0.52 2.76 24 moderately conservative 153634 17p13 CD68 antigen 564 rs17607 CD68 968 17 7425506 NM_001251 NP_001242 A/G A340T plus 20219 1303 SEQUENOM CEPH CEPH (92) 92 0.06 0.06 0.01 250 3 63 "HapMap,freq" Benign 0.227 7 Tolerant 0.52 2.76 24 moderately conservative 153634 17p13 CD68 antigen 565 rs17608 CLC 1178 19 44917486 NM_001828 NP_001819 C/T A28V minus 20220 523 WIAF-CSNP WIAF-CSNP-MITOGPOP4 "Europeans (20), Asians (10) and African-Americans (10)" 38 0.33 0.37 0.06 272 5 0.28 0.1 138 4 123 by freq Tolerant 0.53 2.77 24 moderately conservative 153310 19q13.1 Charcot-Leyden crystal protein 566 rs17608 CLC 1178 19 44917486 NM_001828 NP_001819 C/T A28V minus 477759 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.21 0.37 0.06 272 5 0.28 0.1 138 4 123 by freq Tolerant 0.53 2.77 24 moderately conservative 153310 19q13.1 Charcot-Leyden crystal protein 567 rs17608 CLC 1178 19 44917486 NM_001828 NP_001819 C/T A28V minus 477759 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 82 0.33 0.37 0.06 272 5 0.28 0.1 138 4 123 by freq Tolerant 0.53 2.77 24 moderately conservative 153310 19q13.1 Charcot-Leyden crystal protein 568 rs17608 CLC 1178 19 44917486 NM_001828 NP_001819 C/T A28V minus 477759 1303 SEQUENOM CEPH CEPH (92) 92 0.41 0.37 0.06 272 5 0.28 0.1 138 4 123 by freq Tolerant 0.53 2.77 24 moderately conservative 153310 19q13.1 Charcot-Leyden crystal protein 569 rs17608 CLC 1178 19 44917486 NM_001828 NP_001819 C/T A28V minus 24683968 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.43 0.37 0.06 272 5 0.28 0.1 138 4 123 by freq Tolerant 0.53 2.77 24 moderately conservative 153310 19q13.1 Charcot-Leyden crystal protein 570 rs17611 C5 727 9 120848754 NM_001735 NP_001726 A/G V802I minus 20223 523 WIAF-CSNP WIAF-CSNP-MITOGPOP4 "Europeans (20), Asians (10) and African-Americans (10)" 40 0.33 0.36 0.02 160 2 0.5 0 1462 1 121 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 0.26 2.8 12 conservative 120900 9q33-q34 complement component 5 571 rs17611 C5 727 9 120848754 NM_001735 NP_001726 A/G V802I minus 4094354 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.37 0.36 0.02 160 2 0.5 0 1462 1 121 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 0.26 2.8 12 conservative 120900 9q33-q34 complement component 5 572 rs17655 ERCC5 2073 13 102326003 NM_000123 NP_000114 C/G D1104H minus 2924028 506 NCBI NIHPDR NIHPDR 80 0.46 0.31 0.1 612 7 0.34 0.07 413 6 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 133530 13q22 "excision repair cross-complementing rodent repair deficiency, complementation group 5 (xeroderma pigmentosum, complementation group G (Cockayne syndrome))" 573 rs17655 ERCC5 2073 13 102326003 NM_000123 NP_000114 C/G D1104H minus 3172481 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 40 0.28 0.31 0.1 612 7 0.34 0.07 413 6 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 133530 13q22 "excision repair cross-complementing rodent repair deficiency, complementation group 5 (xeroderma pigmentosum, complementation group G (Cockayne syndrome))" 574 rs17655 ERCC5 2073 13 102326003 NM_000123 NP_000114 C/G D1104H minus 5586520 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.15 0.31 0.1 612 7 0.34 0.07 413 6 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 133530 13q22 "excision repair cross-complementing rodent repair deficiency, complementation group 5 (xeroderma pigmentosum, complementation group G (Cockayne syndrome))" 575 rs17655 ERCC5 2073 13 102326003 NM_000123 NP_000114 C/G D1104H minus 5605326 693 EGP_SNPS PDR90 NIHPDR 178 0.38 0.31 0.1 612 7 0.34 0.07 413 6 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 133530 13q22 "excision repair cross-complementing rodent repair deficiency, complementation group 5 (xeroderma pigmentosum, complementation group G (Cockayne syndrome))" 576 rs17655 ERCC5 2073 13 102326003 NM_000123 NP_000114 C/G D1104H minus 5605326 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.27 0.31 0.1 612 7 0.34 0.07 413 6 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 133530 13q22 "excision repair cross-complementing rodent repair deficiency, complementation group 5 (xeroderma pigmentosum, complementation group G (Cockayne syndrome))" 577 rs17655 ERCC5 2073 13 102326003 NM_000123 NP_000114 C/G D1104H minus 5605326 1303 SEQUENOM CEPH CEPH (92) 92 0.21 0.31 0.1 612 7 0.34 0.07 413 6 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 133530 13q22 "excision repair cross-complementing rodent repair deficiency, complementation group 5 (xeroderma pigmentosum, complementation group G (Cockayne syndrome))" 578 rs17655 ERCC5 2073 13 102326003 NM_000123 NP_000114 C/G D1104H minus 23280293 1371 PERLEGEN AFD_EUR_PANEL European American (24) 40 0.25 0.31 0.1 612 7 0.34 0.07 413 6 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 133530 13q22 "excision repair cross-complementing rodent repair deficiency, complementation group 5 (xeroderma pigmentosum, complementation group G (Cockayne syndrome))" 579 rs20541 IL13 3596 5 132023863 NM_002188 NP_002179 C/T Q144R minus 23200 523 WIAF-CSNP WIAF-CSNP-MITOGPOP4 "Europeans (20), Asians (10) and African-Americans (10)" 36 0.33 0.23 0.07 230 5 0.2 0.06 482 7 123 "by doubleHit,freq,cluster" Potentially damaging 1.318 8 conservative 147683 5q31 interleukin 13 580 rs20541 IL13 3596 5 132023863 NM_002188 NP_002179 C/T Q144R minus 2981853 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 44 0.27 0.23 0.07 230 5 0.2 0.06 482 7 123 "by doubleHit,freq,cluster" Potentially damaging 1.318 8 conservative 147683 5q31 interleukin 13 581 rs20541 IL13 3596 5 132023863 NM_002188 NP_002179 C/T Q144R minus 4323324 649 FHCRC POPU1 USA (20) 40 0.23 0.23 0.07 230 5 0.2 0.06 482 7 123 "by doubleHit,freq,cluster" Potentially damaging 1.318 8 conservative 147683 5q31 interleukin 13 582 rs20541 IL13 3596 5 132023863 NM_002188 NP_002179 C/T Q144R minus 5586633 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.15 0.23 0.07 230 5 0.2 0.06 482 7 123 "by doubleHit,freq,cluster" Potentially damaging 1.318 8 conservative 147683 5q31 interleukin 13 583 rs20541 IL13 3596 5 132023863 NM_002188 NP_002179 C/T Q144R minus 24193850 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.23 0.23 0.07 230 5 0.2 0.06 482 7 123 "by doubleHit,freq,cluster" Potentially damaging 1.318 8 conservative 147683 5q31 interleukin 13 584 rs20551 EP300 2033 22 39872508 NM_001429 NP_001420 A/G I997V plus 23214 523 WIAF-CSNP WIAF-CSNP-MITOGPOP4 "Europeans (20), Asians (10) and African-Americans (10)" 40 0.1 0.21 0.15 88 2 0.07 0.02 94 2 123 "by doubleHit,submitter,freq" Tolerant 0.36 3 95 conservative 602700 22q13.2 E1A binding protein p300 585 rs20551 EP300 2033 22 39872508 NM_001429 NP_001420 A/G I997V plus 24542191 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.31 0.21 0.15 88 2 0.07 0.02 94 2 123 "by doubleHit,submitter,freq" Tolerant 0.36 3 95 conservative 602700 22q13.2 E1A binding protein p300 586 rs20559 LAMC1 3915 1 179831217 NM_002293 NP_002284 A/G R1121Q plus 23222 523 WIAF-CSNP WIAF-CSNP-MITOGPOP4 "Europeans (20), Asians (10) and African-Americans (10)" 40 0.1 0.1 0.04 180 3 0.02 0 46 1 123 by freq Benign 0.361 7 Tolerant 0.52 2.87 14 conservative 150290 1q31 "laminin, gamma 1 (formerly LAMB2)" 587 rs20559 LAMC1 3915 1 179831217 NM_002293 NP_002284 A/G R1121Q plus 23222 1303 SEQUENOM CEPH CEPH (92) 92 0.08 0.1 0.04 180 3 0.02 0 46 1 123 by freq Benign 0.361 7 Tolerant 0.52 2.87 14 conservative 150290 1q31 "laminin, gamma 1 (formerly LAMB2)" 588 rs20559 LAMC1 3915 1 179831217 NM_002293 NP_002284 A/G R1121Q plus 24257529 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.1 0.04 180 3 0.02 0 46 1 123 by freq Benign 0.361 7 Tolerant 0.52 2.87 14 conservative 150290 1q31 "laminin, gamma 1 (formerly LAMB2)" 589 rs20571 CA3 761 8 86539249 NM_005181 NP_005172 A/G V31I plus 23235 523 WIAF-CSNP WIAF-CSNP-MITOGPOP4 "Europeans (20), Asians (10) and African-Americans (10)" 40 0.33 0.41 0.06 300 4 0.38 0.06 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.625 119 Tolerant 1 2.79 59 conservative 114750 8q13-q22 "carbonic anhydrase III, muscle specific" 590 rs20571 CA3 761 8 86539249 NM_005181 NP_005172 A/G V31I plus 10425508 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.39 0.41 0.06 300 4 0.38 0.06 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.625 119 Tolerant 1 2.79 59 conservative 114750 8q13-q22 "carbonic anhydrase III, muscle specific" 591 rs20571 CA3 761 8 86539249 NM_005181 NP_005172 A/G V31I plus 10425508 1303 SEQUENOM CEPH CEPH (92) 92 0.49 0.41 0.06 300 4 0.38 0.06 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.625 119 Tolerant 1 2.79 59 conservative 114750 8q13-q22 "carbonic anhydrase III, muscle specific" 592 rs20571 CA3 761 8 86539249 NM_005181 NP_005172 A/G V31I plus 24025169 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.4 0.41 0.06 300 4 0.38 0.06 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.625 119 Tolerant 1 2.79 59 conservative 114750 8q13-q22 "carbonic anhydrase III, muscle specific" 593 rs20577 TNFRSF10A 8797 8 23138422 NM_003844 NP_003835 C/T T33I minus 23242 523 WIAF-CSNP WIAF-CSNP-MITOGPOP4 "Europeans (20), Asians (10) and African-Americans (10)" 38 0.33 0.33 0 38 1 67 by freq moderately conservative 603611 8p21 "tumor necrosis factor receptor superfamily, member 10a" 594 rs25487 XRCC1 7515 19 48747566 NM_006297 NP_006288 A/G Q399R minus 3254965 506 NCBI NIHPDR NIHPDR 844 0.27 0.29 0.07 1166 4 0.34 0.12 369 5 121 "by cluster,freq" Benign 0.059 8 conservative 194360 19q13.2 X-ray repair complementing defective repair in Chinese hamster cells 1 595 rs25487 XRCC1 7515 19 48747566 NM_006297 NP_006288 A/G Q399R minus 4473996 693 EGP_SNPS PDR90 NIHPDR 168 0.23 0.29 0.07 1166 4 0.34 0.12 369 5 121 "by cluster,freq" Benign 0.059 8 conservative 194360 19q13.2 X-ray repair complementing defective repair in Chinese hamster cells 1 596 rs25487 XRCC1 7515 19 48747566 NM_006297 NP_006288 A/G Q399R minus 4473996 1303 SEQUENOM CEPH CEPH (92) 92 0.42 0.29 0.07 1166 4 0.34 0.12 369 5 121 "by cluster,freq" Benign 0.059 8 conservative 194360 19q13.2 X-ray repair complementing defective repair in Chinese hamster cells 1 597 rs25487 XRCC1 7515 19 48747566 NM_006297 NP_006288 A/G Q399R minus 5586970 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.47 0.29 0.07 1166 4 0.34 0.12 369 5 121 "by cluster,freq" Benign 0.059 8 conservative 194360 19q13.2 X-ray repair complementing defective repair in Chinese hamster cells 1 598 rs25489 XRCC1 7515 19 48748252 NM_006297 NP_006288 A/G R280H minus 3176721 619 WICVAR MITOGPOP6 CORIELL Mixed 56 0.07 0.07 0.02 1110 4 0.06 0.07 349 5 116 "by cluster,freq" Possibly damaging 1.62 8 Tolerant 0.4 2.97 24 conservative 194360 19q13.2 X-ray repair complementing defective repair in Chinese hamster cells 1 599 rs25489 XRCC1 7515 19 48748252 NM_006297 NP_006288 A/G R280H minus 3254966 506 NCBI NIHPDR NIHPDR 818 0.07 0.07 0.02 1110 4 0.06 0.07 349 5 116 "by cluster,freq" Possibly damaging 1.62 8 Tolerant 0.4 2.97 24 conservative 194360 19q13.2 X-ray repair complementing defective repair in Chinese hamster cells 1 600 rs25489 XRCC1 7515 19 48748252 NM_006297 NP_006288 A/G R280H minus 4473987 693 EGP_SNPS PDR90 NIHPDR 174 0.1 0.07 0.02 1110 4 0.06 0.07 349 5 116 "by cluster,freq" Possibly damaging 1.62 8 Tolerant 0.4 2.97 24 conservative 194360 19q13.2 X-ray repair complementing defective repair in Chinese hamster cells 1 601 rs25489 XRCC1 7515 19 48748252 NM_006297 NP_006288 A/G R280H minus 5586971 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.03 0.07 0.02 1110 4 0.06 0.07 349 5 116 "by cluster,freq" Possibly damaging 1.62 8 Tolerant 0.4 2.97 24 conservative 194360 19q13.2 X-ray repair complementing defective repair in Chinese hamster cells 1 602 rs25490 XRCC1 7515 19 48748181 NM_006297 NP_006288 A/G T304A minus 4473989 693 EGP_SNPS PDR90 NIHPDR 172 0.01 0.01 0 172 1 0.02 0.06 299 4 113 "by cluster,freq" Borderline 1.038 8 Tolerant 0.73 2.98 22 moderately conservative 194360 19q13.2 X-ray repair complementing defective repair in Chinese hamster cells 1 603 rs25491 XRCC1 7515 19 48748166 NM_006297 NP_006288 C/T P309S minus 4473990 693 EGP_SNPS PDR90 NIHPDR 176 0.01 0.01 0 176 1 0.5 0 2 1 116 "by cluster,freq" Benign 0.244 8 Tolerant 0.7 3.01 22 moderately conservative 194360 19q13.2 X-ray repair complementing defective repair in Chinese hamster cells 1 604 rs25496 XRCC1 7515 19 48756942 NM_006297 NP_006288 C/T V72A minus 3254957 506 NCBI NIHPDR NIHPDR 866 0.02 0.02 0.01 1040 2 0.5 0 2 1 116 "HapMap,freq,cluster" Possibly damaging 1.51 7 moderately conservative 194360 19q13.2 X-ray repair complementing defective repair in Chinese hamster cells 1 605 rs25496 XRCC1 7515 19 48756942 NM_006297 NP_006288 C/T V72A minus 4473929 693 EGP_SNPS PDR90 NIHPDR 174 0.03 0.02 0.01 1040 2 0.5 0 2 1 116 "HapMap,freq,cluster" Possibly damaging 1.51 7 moderately conservative 194360 19q13.2 X-ray repair complementing defective repair in Chinese hamster cells 1 606 rs25640 HSD17B4 3295 5 118839432 NM_000414 NP_000405 A/G R106H plus 28362 523 WIAF-CSNP WIAF-CSNP-MITOGPOP4 "Europeans (20), Asians (10) and African-Americans (10)" 36 0.33 0.43 0.07 250 4 0.4 0.04 1570 3 123 "HapMap,doubleHit,submitter,freq,cluster" Possibly damaging 1.99 18 Intolerant 0.03 2.84 50 conservative 601860 5q21 hydroxysteroid (17-beta) dehydrogenase 4 607 rs25640 HSD17B4 3295 5 118839432 NM_000414 NP_000405 A/G R106H plus 28362 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 50 0.36 0.43 0.07 250 4 0.4 0.04 1570 3 123 "HapMap,doubleHit,submitter,freq,cluster" Possibly damaging 1.99 18 Intolerant 0.03 2.84 50 conservative 601860 5q21 hydroxysteroid (17-beta) dehydrogenase 4 608 rs25640 HSD17B4 3295 5 118839432 NM_000414 NP_000405 A/G R106H plus 3447822 885 TSC-CSHL HapMap-CEPH-30-trios 116 0.47 0.43 0.07 250 4 0.4 0.04 1570 3 123 "HapMap,doubleHit,submitter,freq,cluster" Possibly damaging 1.99 18 Intolerant 0.03 2.84 50 conservative 601860 5q21 hydroxysteroid (17-beta) dehydrogenase 4 609 rs25640 HSD17B4 3295 5 118839432 NM_000414 NP_000405 A/G R106H plus 24346051 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.48 0.43 0.07 250 4 0.4 0.04 1570 3 123 "HapMap,doubleHit,submitter,freq,cluster" Possibly damaging 1.99 18 Intolerant 0.03 2.84 50 conservative 601860 5q21 hydroxysteroid (17-beta) dehydrogenase 4 610 rs25644 P2RX4 5025 12 120129366 NM_002560 NP_002551 A/G S242G plus 28367 523 WIAF-CSNP WIAF-CSNP-MITOGPOP4 "Europeans (20), Asians (10) and African-Americans (10)" 60 0.1 0.08 0.03 352 4 0.2 0.04 1596 3 123 "by cluster,freq" Borderline 1.224 30 Intolerant 0.05 2.81 63 moderately conservative 600846 12q24.32 "purinergic receptor P2X, ligand-gated ion channel, 4" 611 rs25644 P2RX4 5025 12 120129366 NM_002560 NP_002551 A/G S242G plus 3178007 619 WICVAR MITOGPOP6 CORIELL Mixed 60 0.12 0.08 0.03 352 4 0.2 0.04 1596 3 123 "by cluster,freq" Borderline 1.224 30 Intolerant 0.05 2.81 63 moderately conservative 600846 12q24.32 "purinergic receptor P2X, ligand-gated ion channel, 4" 612 rs25644 P2RX4 5025 12 120129366 NM_002560 NP_002551 A/G S242G plus 23933567 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.08 0.03 352 4 0.2 0.04 1596 3 123 "by cluster,freq" Borderline 1.224 30 Intolerant 0.05 2.81 63 moderately conservative 600846 12q24.32 "purinergic receptor P2X, ligand-gated ion channel, 4" 613 rs25644 P2RX4 5025 12 120129366 NM_002560 NP_002551 A/G S242G plus 24811130 1303 SEQUENOM CEPH CEPH (92) 184 0.08 0.08 0.03 352 4 0.2 0.04 1596 3 123 "by cluster,freq" Borderline 1.224 30 Intolerant 0.05 2.81 63 moderately conservative 600846 12q24.32 "purinergic receptor P2X, ligand-gated ion channel, 4" 614 rs25653 ANPEP 290 15 88150562 NM_001150 NP_001141 A/G R86Q minus 28376 523 WIAF-CSNP WIAF-CSNP-MITOGPOP4 "Europeans (20), Asians (10) and African-Americans (10)" 38 0.33 0.42 0.04 326 5 0.42 0.06 1566 3 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.116 12 conservative 151530 15q25-q26 "alanyl (membrane) aminopeptidase (aminopeptidase N, aminopeptidase M, microsomal aminopeptidase, CD13, p150)" 615 rs25653 ANPEP 290 15 88150562 NM_001150 NP_001141 A/G R86Q minus 28376 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 32 0.47 0.42 0.04 326 5 0.42 0.06 1566 3 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.116 12 conservative 151530 15q25-q26 "alanyl (membrane) aminopeptidase (aminopeptidase N, aminopeptidase M, microsomal aminopeptidase, CD13, p150)" 616 rs25653 ANPEP 290 15 88150562 NM_001150 NP_001141 A/G R86Q minus 12586497 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.43 0.42 0.04 326 5 0.42 0.06 1566 3 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.116 12 conservative 151530 15q25-q26 "alanyl (membrane) aminopeptidase (aminopeptidase N, aminopeptidase M, microsomal aminopeptidase, CD13, p150)" 617 rs25653 ANPEP 290 15 88150562 NM_001150 NP_001141 A/G R86Q minus 12586497 1303 SEQUENOM CEPH CEPH (92) 92 0.44 0.42 0.04 326 5 0.42 0.06 1566 3 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.116 12 conservative 151530 15q25-q26 "alanyl (membrane) aminopeptidase (aminopeptidase N, aminopeptidase M, microsomal aminopeptidase, CD13, p150)" 618 rs25653 ANPEP 290 15 88150562 NM_001150 NP_001141 A/G R86Q minus 24057941 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.41 0.42 0.04 326 5 0.42 0.06 1566 3 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.116 12 conservative 151530 15q25-q26 "alanyl (membrane) aminopeptidase (aminopeptidase N, aminopeptidase M, microsomal aminopeptidase, CD13, p150)" 619 rs25655 CAPN2 824 1 220207143 NM_001748 NP_001739 C/G D22E plus 28378 523 WIAF-CSNP WIAF-CSNP-MITOGPOP4 "Europeans (20), Asians (10) and African-Americans (10)" 40 0.1 0.06 0.05 100 2 123 by freq Benign 0.01 59 conservative 114230 1q41-q42 "calpain 2, (m/II) large subunit" 620 rs25655 CAPN2 824 1 220207143 NM_001748 NP_001739 C/G D22E plus 28378 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 60 0.03 0.06 0.05 100 2 123 by freq Benign 0.01 59 conservative 114230 1q41-q42 "calpain 2, (m/II) large subunit" 621 rs25680 TNFRSF7 939 12 6424889 NM_001242 NP_001233 A/G A59T plus 28404 523 WIAF-CSNP WIAF-CSNP-MITOGPOP4 "Europeans (20), Asians (10) and African-Americans (10)" 38 0.33 0.22 0.11 646 9 0.12 0.02 236 5 123 "HapMap,freq" Tolerant 0.28 2.93 10 moderately conservative 186711 12p13 "tumor necrosis factor receptor superfamily, member 7" 622 rs25680 TNFRSF7 939 12 6424889 NM_001242 NP_001233 A/G A59T plus 28404 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 54 0.07 0.22 0.11 646 9 0.12 0.02 236 5 123 "HapMap,freq" Tolerant 0.28 2.93 10 moderately conservative 186711 12p13 "tumor necrosis factor receptor superfamily, member 7" 623 rs25680 TNFRSF7 939 12 6424889 NM_001242 NP_001233 A/G A59T plus 131069 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 84 0.29 0.22 0.11 646 9 0.12 0.02 236 5 123 "HapMap,freq" Tolerant 0.28 2.93 10 moderately conservative 186711 12p13 "tumor necrosis factor receptor superfamily, member 7" 624 rs25680 TNFRSF7 939 12 6424889 NM_001242 NP_001233 A/G A59T plus 131069 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.18 0.22 0.11 646 9 0.12 0.02 236 5 123 "HapMap,freq" Tolerant 0.28 2.93 10 moderately conservative 186711 12p13 "tumor necrosis factor receptor superfamily, member 7" 625 rs25680 TNFRSF7 939 12 6424889 NM_001242 NP_001233 A/G A59T plus 131069 902 AFFY Caucasian 18 0.22 0.22 0.11 646 9 0.12 0.02 236 5 123 "HapMap,freq" Tolerant 0.28 2.93 10 moderately conservative 186711 12p13 "tumor necrosis factor receptor superfamily, member 7" 626 rs25680 TNFRSF7 939 12 6424889 NM_001242 NP_001233 A/G A59T plus 131069 904 AFFY CEPH 12 0.08 0.22 0.11 646 9 0.12 0.02 236 5 123 "HapMap,freq" Tolerant 0.28 2.93 10 moderately conservative 186711 12p13 "tumor necrosis factor receptor superfamily, member 7" 627 rs25680 TNFRSF7 939 12 6424889 NM_001242 NP_001233 A/G A59T plus 131069 1303 SEQUENOM CEPH CEPH (92) 92 0.42 0.22 0.11 646 9 0.12 0.02 236 5 123 "HapMap,freq" Tolerant 0.28 2.93 10 moderately conservative 186711 12p13 "tumor necrosis factor receptor superfamily, member 7" 628 rs25680 TNFRSF7 939 12 6424889 NM_001242 NP_001233 A/G A59T plus 16340789 693 EGP_SNPS PDR90 NIHPDR 180 0.14 0.22 0.11 646 9 0.12 0.02 236 5 123 "HapMap,freq" Tolerant 0.28 2.93 10 moderately conservative 186711 12p13 "tumor necrosis factor receptor superfamily, member 7" 629 rs25680 TNFRSF7 939 12 6424889 NM_001242 NP_001233 A/G A59T plus 24697307 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.25 0.22 0.11 646 9 0.12 0.02 236 5 123 "HapMap,freq" Tolerant 0.28 2.93 10 moderately conservative 186711 12p13 "tumor necrosis factor receptor superfamily, member 7" 630 rs25683 ACAT2 39 6 160166754 NM_005891 NP_005882 A/G K211R plus 28408 523 WIAF-CSNP WIAF-CSNP-MITOGPOP4 "Europeans (20), Asians (10) and African-Americans (10)" 40 0.33 0.25 0.1 88 2 0.18 0 1468 1 102 "by cluster,freq" Benign 0.715 106 Potentially intolerant 0.1 2.75 148 conservative 100678 6q25.3-q26 acetyl-Coenzyme A acetyltransferase 2 (acetoacetyl Coenzyme A thiolase) 631 rs25683 ACAT2 39 6 160166754 NM_005891 NP_005882 A/G K211R plus 28408 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 48 0.19 0.25 0.1 88 2 0.18 0 1468 1 102 "by cluster,freq" Benign 0.715 106 Potentially intolerant 0.1 2.75 148 conservative 100678 6q25.3-q26 acetyl-Coenzyme A acetyltransferase 2 (acetoacetyl Coenzyme A thiolase) 632 rs25882 CSF2 1437 5 131439359 NM_000758 NP_000749 C/T I117T plus 2981718 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.2 0.23 0.05 204 4 0.33 0.05 486 7 123 "by submitter,freq,cluster" Benign 0.092 25 moderately conservative 138960 5q31.1 colony stimulating factor 2 (granulocyte-macrophage) 633 rs25882 CSF2 1437 5 131439359 NM_000758 NP_000749 C/T I117T plus 3176020 619 WICVAR MITOGPOP6 CORIELL Mixed 48 0.29 0.23 0.05 204 4 0.33 0.05 486 7 123 "by submitter,freq,cluster" Benign 0.092 25 moderately conservative 138960 5q31.1 colony stimulating factor 2 (granulocyte-macrophage) 634 rs25882 CSF2 1437 5 131439359 NM_000758 NP_000749 C/T I117T plus 6903720 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.24 0.23 0.05 204 4 0.33 0.05 486 7 123 "by submitter,freq,cluster" Benign 0.092 25 moderately conservative 138960 5q31.1 colony stimulating factor 2 (granulocyte-macrophage) 635 rs25882 CSF2 1437 5 131439359 NM_000758 NP_000749 C/T I117T plus 23737224 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.17 0.23 0.05 204 4 0.33 0.05 486 7 123 "by submitter,freq,cluster" Benign 0.092 25 moderately conservative 138960 5q31.1 colony stimulating factor 2 (granulocyte-macrophage) 636 rs27230 ZNF434 54925 16 3374700 NM_017810 NP_060280 A/G Y120H plus 24479903 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.27 0.27 0 48 1 123 "by submitter,freq" Intolerant 0 3.02 13 moderately conservative 16p13.3 zinc finger protein 434 637 rs30461 IL29 282618 19 44480955 NM_172140 NP_742152 C/T N188D minus 689370 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.12 0.13 0.02 168 2 0.19 0.22 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Potentially damaging 1.436 8 conservative 607403 19q13.13 "interleukin 29 (interferon, lambda 1)" 638 rs30461 IL29 282618 19 44480955 NM_172140 NP_742152 C/T N188D minus 23763490 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.13 0.02 168 2 0.19 0.22 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Potentially damaging 1.436 8 conservative 607403 19q13.13 "interleukin 29 (interferon, lambda 1)" 639 rs30489 TCF7 6932 5 133509366 NM_201633 NP_963964 C/T G256R minus 3576863 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.05 0.04 0.03 260 3 0.17 0.21 94 2 123 "HapMap,submitter,freq,cluster" moderately radical 189908 5q31.1 "transcription factor 7 (T-cell specific, HMG-box)" 640 rs30489 TCF7 6932 5 133509366 NM_201633 NP_963964 C/T G256R minus 3576863 1303 SEQUENOM CEPH CEPH (92) 92 0.01 0.04 0.03 260 3 0.17 0.21 94 2 123 "HapMap,submitter,freq,cluster" moderately radical 189908 5q31.1 "transcription factor 7 (T-cell specific, HMG-box)" 641 rs30489 TCF7 6932 5 133509366 NM_201633 NP_963964 C/T G256R minus 23953339 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.04 0.03 260 3 0.17 0.21 94 2 123 "HapMap,submitter,freq,cluster" moderately radical 189908 5q31.1 "transcription factor 7 (T-cell specific, HMG-box)" 642 rs30842 GOT2 2806 16 57300955 NM_002080 NP_002071 G/T V346G minus 10819561 1303 SEQUENOM CEPH CEPH (92) 92 0.49 0.45 0.07 140 2 0.19 0.14 94 2 123 "by cluster,freq" Benign 0.67 67 moderately radical 138150 16q21 "glutamic-oxaloacetic transaminase 2, mitochondrial (aspartate aminotransferase 2)" 643 rs30842 GOT2 2806 16 57300955 NM_002080 NP_002071 G/T V346G minus 24614222 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.38 0.45 0.07 140 2 0.19 0.14 94 2 123 "by cluster,freq" Benign 0.67 67 moderately radical 138150 16q21 "glutamic-oxaloacetic transaminase 2, mitochondrial (aspartate aminotransferase 2)" 644 rs31849 PCDHB3 56132 5 140460539 NM_018937 NP_061760 C/T K41R minus 23350582 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.09 0.09 0 46 1 0.07 0.03 90 2 123 "by doubleHit,freq,cluster" Benign 0.483 97 Tolerant 0.45 2.78 123 conservative 606329 5q31 protocadherin beta 3 645 rs31853 PCDHB2 56133 5 140454940 NM_018936 NP_061759 A/G V128I plus 1335672 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 82 0.12 0.09 0.04 336 4 0.08 0.03 1522 5 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.625 98 Tolerant 1 2.77 126 conservative 606328 5q31 protocadherin beta 2 646 rs31853 PCDHB2 56133 5 140454940 NM_018936 NP_061759 A/G V128I plus 1335672 885 TSC-CSHL HapMap-CEPH-30-trios 114 0.05 0.09 0.04 336 4 0.08 0.03 1522 5 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.625 98 Tolerant 1 2.77 126 conservative 606328 5q31 protocadherin beta 2 647 rs31853 PCDHB2 56133 5 140454940 NM_018936 NP_061759 A/G V128I plus 1335672 1303 SEQUENOM CEPH CEPH (92) 92 0.12 0.09 0.04 336 4 0.08 0.03 1522 5 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.625 98 Tolerant 1 2.77 126 conservative 606328 5q31 protocadherin beta 2 648 rs31853 PCDHB2 56133 5 140454940 NM_018936 NP_061759 A/G V128I plus 23350563 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.09 0.04 336 4 0.08 0.03 1522 5 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.625 98 Tolerant 1 2.77 126 conservative 606328 5q31 protocadherin beta 2 649 rs34899 RHOBTB3 22836 5 95116957 NM_014899 NP_055714 A/G N262D plus 1788541 1303 SEQUENOM CEPH CEPH (92) 92 0.21 0.21 0 92 1 121 "by doubleHit,submitter,freq,cluster" conservative 607353 5q15 Rho-related BTB domain containing 3 650 rs36259 LASS4 79603 19 8232904 NM_024552 NP_078828 A/G A366T plus 496166 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.22 0.2 0.03 259 3 0.18 0.04 1590 3 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 19p13.3 LAG1 longevity assurance homolog 4 (S. cerevisiae) 651 rs36259 LASS4 79603 19 8232904 NM_024552 NP_078828 A/G A366T plus 496166 1303 SEQUENOM CEPH CEPH (92) 93 0.16 0.2 0.03 259 3 0.18 0.04 1590 3 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 19p13.3 LAG1 longevity assurance homolog 4 (S. cerevisiae) 652 rs36259 LASS4 79603 19 8232904 NM_024552 NP_078828 A/G A366T plus 23582637 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.2 0.03 259 3 0.18 0.04 1590 3 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 19p13.3 LAG1 longevity assurance homolog 4 (S. cerevisiae) 653 rs37369 AGXT2 64902 5 35072872 NM_031900 NP_114106 C/T V140I plus 14655015 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.11 0.11 0.02 260 3 0.36 0.03 1592 3 123 "HapMap,submitter,freq,cluster" Benign 0.3 8 Tolerant 1 2.77 36 conservative 5p13 alanine-glyoxylate aminotransferase 2 654 rs37369 AGXT2 64902 5 35072872 NM_031900 NP_114106 C/T V140I plus 14655015 1303 SEQUENOM CEPH CEPH (92) 92 0.13 0.11 0.02 260 3 0.36 0.03 1592 3 123 "HapMap,submitter,freq,cluster" Benign 0.3 8 Tolerant 1 2.77 36 conservative 5p13 alanine-glyoxylate aminotransferase 2 655 rs37369 AGXT2 64902 5 35072872 NM_031900 NP_114106 C/T V140I plus 23986321 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.11 0.02 260 3 0.36 0.03 1592 3 123 "HapMap,submitter,freq,cluster" Benign 0.3 8 Tolerant 1 2.77 36 conservative 5p13 alanine-glyoxylate aminotransferase 2 656 rs40401 IL3 3562 5 131424377 NM_000588 NP_000579 C/T P27S plus 830808 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.21 0.23 0.04 342 5 0.42 0.02 1620 4 123 "HapMap,doubleHit,freq,cluster" moderately conservative 147740 5q31.1 "interleukin 3 (colony-stimulating factor, multiple)" 657 rs40401 IL3 3562 5 131424377 NM_000588 NP_000579 C/T P27S plus 830808 1303 SEQUENOM CEPH CEPH (92) 92 0.19 0.23 0.04 342 5 0.42 0.02 1620 4 123 "HapMap,doubleHit,freq,cluster" moderately conservative 147740 5q31.1 "interleukin 3 (colony-stimulating factor, multiple)" 658 rs40401 IL3 3562 5 131424377 NM_000588 NP_000579 C/T P27S plus 2981902 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.26 0.23 0.04 342 5 0.42 0.02 1620 4 123 "HapMap,doubleHit,freq,cluster" moderately conservative 147740 5q31.1 "interleukin 3 (colony-stimulating factor, multiple)" 659 rs40401 IL3 3562 5 131424377 NM_000588 NP_000579 C/T P27S plus 4323372 649 FHCRC POPU1 USA (20) 40 0.3 0.23 0.04 342 5 0.42 0.02 1620 4 123 "HapMap,doubleHit,freq,cluster" moderately conservative 147740 5q31.1 "interleukin 3 (colony-stimulating factor, multiple)" 660 rs40401 IL3 3562 5 131424377 NM_000588 NP_000579 C/T P27S plus 23737132 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.24 0.23 0.04 342 5 0.42 0.02 1620 4 123 "HapMap,doubleHit,freq,cluster" moderately conservative 147740 5q31.1 "interleukin 3 (colony-stimulating factor, multiple)" 661 rs42524 COL1A2 1278 7 93687890 NM_000089 NP_000080 C/G P549A plus 3127654 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 83 0.31 0.37 0.08 175 2 0.19 0.07 166 2 121 "by cluster,freq" Tolerant 0.82 3.04 78 conservative 120160 7q22.1 "collagen, type I, alpha 2" 662 rs42524 COL1A2 1278 7 93687890 NM_000089 NP_000080 C/G P549A plus 3127654 1303 SEQUENOM CEPH CEPH (92) 92 0.42 0.37 0.08 175 2 0.19 0.07 166 2 121 "by cluster,freq" Tolerant 0.82 3.04 78 conservative 120160 7q22.1 "collagen, type I, alpha 2" 663 rs42942 PES1 23481 22 29301907 NM_014303 NP_055118 A/T T264S plus 13383550 1303 SEQUENOM CEPH CEPH (92) 92 0.04 0.04 0 92 1 120 by freq Benign 0.895 9 Tolerant 0.75 2.87 20 moderately conservative 605819 22q12.1 "pescadillo homolog 1, containing BRCT domain (zebrafish)" 664 rs103612 NUP214 8021 9 131049646 NM_005085 NP_005076 C/T P574S plus 110164 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.32 0.36 0.05 260 3 0.34 0.01 94 2 123 "HapMap,doubleHit,freq,cluster" Benign 0.442 5 moderately conservative 114350 9q34.1 nucleoporin 214kDa 665 rs103612 NUP214 8021 9 131049646 NM_005085 NP_005076 C/T P574S plus 110164 1303 SEQUENOM CEPH CEPH (92) 92 0.4 0.36 0.05 260 3 0.34 0.01 94 2 123 "HapMap,doubleHit,freq,cluster" Benign 0.442 5 moderately conservative 114350 9q34.1 nucleoporin 214kDa 666 rs103612 NUP214 8021 9 131049646 NM_005085 NP_005076 C/T P574S plus 24555978 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.4 0.36 0.05 260 3 0.34 0.01 94 2 123 "HapMap,doubleHit,freq,cluster" Benign 0.442 5 moderately conservative 114350 9q34.1 nucleoporin 214kDa 667 rs132653 APOL3 80833 22 34881323 NM_145640 NP_663615 A/C S39R minus 1465169 760 TSC-CSHL CEL_CAUCASIAN CELERA Caucasians (30) 56 0.18 0.17 0.04 320 4 0.15 0.22 265 5 123 "HapMap,doubleHit,submitter,freq,cluster" moderately radical 607253 22q13.1 "apolipoprotein L, 3" 668 rs132653 APOL3 80833 22 34881323 NM_145640 NP_663615 A/C S39R minus 1465169 782 TSC-CSHL WICGR6_CAUCASIAN_POOLED WICGR Caucasian (48) 96 0.17 0.17 0.04 320 4 0.15 0.22 265 5 123 "HapMap,doubleHit,submitter,freq,cluster" moderately radical 607253 22q13.1 "apolipoprotein L, 3" 669 rs132653 APOL3 80833 22 34881323 NM_145640 NP_663615 A/C S39R minus 1465169 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.14 0.17 0.04 320 4 0.15 0.22 265 5 123 "HapMap,doubleHit,submitter,freq,cluster" moderately radical 607253 22q13.1 "apolipoprotein L, 3" 670 rs132653 APOL3 80833 22 34881323 NM_145640 NP_663615 A/C S39R minus 23644163 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.25 0.17 0.04 320 4 0.15 0.22 265 5 123 "HapMap,doubleHit,submitter,freq,cluster" moderately radical 607253 22q13.1 "apolipoprotein L, 3" 671 rs133885 MYO18B 84700 22 24483843 NM_032608 NP_115997 A/G G44E plus 24581329 1371 PERLEGEN AFD_EUR_PANEL European American (24) 44 0.07 0.07 0 44 1 0.02 0 46 1 123 "by doubleHit,freq" moderately conservative 607295 22q11.2-q12.1 myosin XVIIIB 672 rs136467 RFPL2 10739 22 30911408 NM_006605 NP_006596 C/T V258I plus 8288357 1303 SEQUENOM CEPH CEPH (92) 92 0.18 0.18 0 92 1 123 "by doubleHit,freq,cluster" Benign 0.906 11 conservative 605969 22q12.3 ret finger protein-like 2 673 rs136470 RFPL2 10739 22 30911480 NM_006605 NP_006596 C/T S234G plus 8293332 1303 SEQUENOM CEPH CEPH (92) 92 0.23 0.23 0 92 1 121 "by doubleHit,freq,cluster" Benign 0.006 11 moderately conservative 605969 22q12.3 ret finger protein-like 2 674 rs136478 RFPL2 10739 22 30913577 NM_006605 NP_006596 C/T C51Y plus 144631 1303 SEQUENOM CEPH CEPH (92) 92 0.45 0.45 0 92 1 119 "by doubleHit,freq,cluster" Possibly damaging 1.744 11 radical 605969 22q12.3 ret finger protein-like 2 675 rs140054 GTSE1 51512 22 45042919 NM_016426 NP_057510 A/G W506R minus 8021617 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.08 0.14 0.09 212 2 121 "HapMap,submitter,freq,cluster" moderately radical 607477 22q13.2-q13.3 G-2 and S-phase expressed 1 676 rs140054 GTSE1 51512 22 45042919 NM_016426 NP_057510 A/G W506R minus 8021617 1303 SEQUENOM CEPH CEPH (92) 92 0.21 0.14 0.09 212 2 121 "HapMap,submitter,freq,cluster" moderately radical 607477 22q13.2-q13.3 G-2 and S-phase expressed 1 677 rs140693 MBD4 8930 3 130638149 NM_003925 NP_003916 A/G E346K minus 149192 524 LDN AUTISM USA (autistic probands) 24 0.09 0.08 0.01 1074 3 0.23 0.3 94 2 123 "by submitter,freq,cluster" moderately conservative 603574 3q21-q22 methyl-CpG binding domain protein 4 678 rs140693 MBD4 8930 3 130638149 NM_003925 NP_003916 A/G E346K minus 3255099 506 NCBI NIHPDR NIHPDR 872 0.08 0.08 0.01 1074 3 0.23 0.3 94 2 123 "by submitter,freq,cluster" moderately conservative 603574 3q21-q22 methyl-CpG binding domain protein 4 679 rs140693 MBD4 8930 3 130638149 NM_003925 NP_003916 A/G E346K minus 4385591 693 EGP_SNPS PDR90 NIHPDR 178 0.07 0.08 0.01 1074 3 0.23 0.3 94 2 123 "by submitter,freq,cluster" moderately conservative 603574 3q21-q22 methyl-CpG binding domain protein 4 680 rs144848 BRCA2 675 13 31804729 NM_000059 NP_000050 G/T N372H minus 153384 902 AFFY Caucasian 14 0.29 0.32 0.06 656 9 0.27 0.09 506 9 123 "by doubleHit,submitter,freq,cluster" Benign 0.229 9 moderately conservative 600185 13q12.3 "breast cancer 2, early onset" 681 rs144848 BRCA2 675 13 31804729 NM_000059 NP_000050 G/T N372H minus 153384 904 AFFY CEPH 12 0.42 0.32 0.06 656 9 0.27 0.09 506 9 123 "by doubleHit,submitter,freq,cluster" Benign 0.229 9 moderately conservative 600185 13q12.3 "breast cancer 2, early onset" 682 rs144848 BRCA2 675 13 31804729 NM_000059 NP_000050 G/T N372H minus 153384 1303 SEQUENOM CEPH CEPH (92) 92 0.37 0.32 0.06 656 9 0.27 0.09 506 9 123 "by doubleHit,submitter,freq,cluster" Benign 0.229 9 moderately conservative 600185 13q12.3 "breast cancer 2, early onset" 683 rs144848 BRCA2 675 13 31804729 NM_000059 NP_000050 G/T N372H minus 887467 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.36 0.32 0.06 656 9 0.27 0.09 506 9 123 "by doubleHit,submitter,freq,cluster" Benign 0.229 9 moderately conservative 600185 13q12.3 "breast cancer 2, early onset" 684 rs144848 BRCA2 675 13 31804729 NM_000059 NP_000050 G/T N372H minus 887467 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 176 0.38 0.32 0.06 656 9 0.27 0.09 506 9 123 "by doubleHit,submitter,freq,cluster" Benign 0.229 9 moderately conservative 600185 13q12.3 "breast cancer 2, early onset" 685 rs144848 BRCA2 675 13 31804729 NM_000059 NP_000050 G/T N372H minus 3172559 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 60 0.23 0.32 0.06 656 9 0.27 0.09 506 9 123 "by doubleHit,submitter,freq,cluster" Benign 0.229 9 moderately conservative 600185 13q12.3 "breast cancer 2, early onset" 686 rs144848 BRCA2 675 13 31804729 NM_000059 NP_000050 G/T N372H minus 5586305 775 SNP500CANCER CAUC1 Caucasian (31) 60 0.28 0.32 0.06 656 9 0.27 0.09 506 9 123 "by doubleHit,submitter,freq,cluster" Benign 0.229 9 moderately conservative 600185 13q12.3 "breast cancer 2, early onset" 687 rs144848 BRCA2 675 13 31804729 NM_000059 NP_000050 G/T N372H minus 16355781 693 EGP_SNPS PDR90 NIHPDR 180 0.26 0.32 0.06 656 9 0.27 0.09 506 9 123 "by doubleHit,submitter,freq,cluster" Benign 0.229 9 moderately conservative 600185 13q12.3 "breast cancer 2, early onset" 688 rs144848 BRCA2 675 13 31804729 NM_000059 NP_000050 G/T N372H minus 24664348 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.38 0.32 0.06 656 9 0.27 0.09 506 9 123 "by doubleHit,submitter,freq,cluster" Benign 0.229 9 moderately conservative 600185 13q12.3 "breast cancer 2, early onset" 689 rs150857 CARKL 23729 17 3473386 NM_013276 NP_037408 C/T E215K plus 4063916 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.09 0.14 0.06 258 3 0.23 0.05 1590 3 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 605060 17p13 carbohydrate kinase-like 690 rs150857 CARKL 23729 17 3473386 NM_013276 NP_037408 C/T E215K plus 4063916 1303 SEQUENOM CEPH CEPH (92) 92 0.19 0.14 0.06 258 3 0.23 0.05 1590 3 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 605060 17p13 carbohydrate kinase-like 691 rs150857 CARKL 23729 17 3473386 NM_013276 NP_037408 C/T E215K plus 23624334 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.14 0.06 258 3 0.23 0.05 1590 3 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 605060 17p13 carbohydrate kinase-like 692 rs156697 GSTO2 119391 10 106029175 NM_183239 NP_899062 C/T N142D minus 773736 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.4 0.38 0.05 278 4 0.25 0.04 892 6 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.401 14 Tolerant 0.87 2.82 26 conservative 10q25.1 glutathione S-transferase omega 2 693 rs156697 GSTO2 119391 10 106029175 NM_183239 NP_899062 C/T N142D minus 773736 1303 SEQUENOM CEPH CEPH (92) 92 0.32 0.38 0.05 278 4 0.25 0.04 892 6 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.401 14 Tolerant 0.87 2.82 26 conservative 10q25.1 glutathione S-transferase omega 2 694 rs156697 GSTO2 119391 10 106029175 NM_183239 NP_899062 C/T N142D minus 16334038 902 AFFY Caucasian 18 0.44 0.38 0.05 278 4 0.25 0.04 892 6 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.401 14 Tolerant 0.87 2.82 26 conservative 10q25.1 glutathione S-transferase omega 2 695 rs156697 GSTO2 119391 10 106029175 NM_183239 NP_899062 C/T N142D minus 24503173 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.42 0.38 0.05 278 4 0.25 0.04 892 6 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.401 14 Tolerant 0.87 2.82 26 conservative 10q25.1 glutathione S-transferase omega 2 696 rs157496 PDZK3 23037 5 32123131 NM_178140 NP_835260 A/G T1274A plus 698075 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.24 0.25 0.1 260 3 0.41 0.07 92 2 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 5p13.3 PDZ domain containing 3 697 rs157496 PDZK3 23037 5 32123131 NM_178140 NP_835260 A/G T1274A plus 698075 1303 SEQUENOM CEPH CEPH (92) 92 0.33 0.25 0.1 260 3 0.41 0.07 92 2 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 5p13.3 PDZ domain containing 3 698 rs157496 PDZK3 23037 5 32123131 NM_178140 NP_835260 A/G T1274A plus 24009438 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.25 0.1 260 3 0.41 0.07 92 2 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 5p13.3 PDZ domain containing 3 699 rs158551 BCAS1 8537 20 52078573 NM_003657 NP_003648 C/T V163A minus 614289 1303 SEQUENOM CEPH CEPH (92) 92 0.1 0.09 0.03 140 2 0.24 0.31 94 2 123 "by cluster,freq" Tolerant 0.73 2.88 10 moderately conservative 602968 20q13.2-q13.3 breast carcinoma amplified sequence 1 700 rs158551 BCAS1 8537 20 52078573 NM_003657 NP_003648 C/T V163A minus 24095060 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.09 0.03 140 2 0.24 0.31 94 2 123 "by cluster,freq" Tolerant 0.73 2.88 10 moderately conservative 602968 20q13.2-q13.3 breast carcinoma amplified sequence 1 701 rs160277 CSPG2 1462 5 82873387 NM_004385 NP_004376 A/C D2937Y minus 666549 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.43 0.37 0.04 272 4 0.45 0.04 1599 5 123 "HapMap,doubleHit,freq,cluster" Benign 0.23 5 Intolerant 0.04 2.79 15 radical 118661 5q14.3 chondroitin sulfate proteoglycan 2 (versican) 702 rs160277 CSPG2 1462 5 82873387 NM_004385 NP_004376 A/C D2937Y minus 666549 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 92 0.34 0.37 0.04 272 4 0.45 0.04 1599 5 123 "HapMap,doubleHit,freq,cluster" Benign 0.23 5 Intolerant 0.04 2.79 15 radical 118661 5q14.3 chondroitin sulfate proteoglycan 2 (versican) 703 rs160277 CSPG2 1462 5 82873387 NM_004385 NP_004376 A/C D2937Y minus 666549 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.35 0.37 0.04 272 4 0.45 0.04 1599 5 123 "HapMap,doubleHit,freq,cluster" Benign 0.23 5 Intolerant 0.04 2.79 15 radical 118661 5q14.3 chondroitin sulfate proteoglycan 2 (versican) 704 rs160277 CSPG2 1462 5 82873387 NM_004385 NP_004376 A/C D2937Y minus 23674326 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.44 0.37 0.04 272 4 0.45 0.04 1599 5 123 "HapMap,doubleHit,freq,cluster" Benign 0.23 5 Intolerant 0.04 2.79 15 radical 118661 5q14.3 chondroitin sulfate proteoglycan 2 (versican) 705 rs160278 CSPG2 1462 5 82871480 NM_004385 NP_004376 A/T F2301Y minus 739666 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.43 0.47 0.03 240 4 0.47 0.05 1598 4 123 "by doubleHit,freq,cluster" Benign 0.172 5 Tolerant 1 3.04 10 conservative 118661 5q14.3 chondroitin sulfate proteoglycan 2 (versican) 706 rs160278 CSPG2 1462 5 82871480 NM_004385 NP_004376 A/T F2301Y minus 739666 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 88 0.47 0.47 0.03 240 4 0.47 0.05 1598 4 123 "by doubleHit,freq,cluster" Benign 0.172 5 Tolerant 1 3.04 10 conservative 118661 5q14.3 chondroitin sulfate proteoglycan 2 (versican) 707 rs160278 CSPG2 1462 5 82871480 NM_004385 NP_004376 A/T F2301Y minus 1295190 1303 SEQUENOM CEPH CEPH (92) 92 0.49 0.47 0.03 240 4 0.47 0.05 1598 4 123 "by doubleHit,freq,cluster" Benign 0.172 5 Tolerant 1 3.04 10 conservative 118661 5q14.3 chondroitin sulfate proteoglycan 2 (versican) 708 rs160278 CSPG2 1462 5 82871480 NM_004385 NP_004376 A/T F2301Y minus 23674325 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.43 0.47 0.03 240 4 0.47 0.05 1598 4 123 "by doubleHit,freq,cluster" Benign 0.172 5 Tolerant 1 3.04 10 conservative 118661 5q14.3 chondroitin sulfate proteoglycan 2 (versican) 709 rs160838 RGL3 57139 19 11387759 XM_290867 XP_290867 C/T A164V minus 1873156 1303 SEQUENOM CEPH CEPH (92) 92 0.47 0.47 0 92 1 121 "by doubleHit,freq,cluster" Tolerant 0.63 2.9 21 moderately conservative 19p13.2 ral guanine nucleotide dissociation stimulator-like 3 710 rs161704 IL31RA 133396 5 55242201 NM_139017 NP_620586 C/T S497N minus 1991445 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 84 0.22 0.28 0.05 252 3 0.35 0.13 258 4 123 "HapMap,doubleHit,freq,cluster" Borderline 1.098 6 Tolerant 0.24 2.8 21 conservative 5q11.2 interleukin 31 receptor A 711 rs161704 IL31RA 133396 5 55242201 NM_139017 NP_620586 C/T S497N minus 1991445 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.3 0.28 0.05 252 3 0.35 0.13 258 4 123 "HapMap,doubleHit,freq,cluster" Borderline 1.098 6 Tolerant 0.24 2.8 21 conservative 5q11.2 interleukin 31 receptor A 712 rs161704 IL31RA 133396 5 55242201 NM_139017 NP_620586 C/T S497N minus 23352578 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.33 0.28 0.05 252 3 0.35 0.13 258 4 123 "HapMap,doubleHit,freq,cluster" Borderline 1.098 6 Tolerant 0.24 2.8 21 conservative 5q11.2 interleukin 31 receptor A 713 rs164075 PCDH12 51294 5 141316448 NM_016580 NP_057664 A/C H385N minus 849396 1303 SEQUENOM CEPH CEPH (92) 92 0.36 0.37 0.03 140 2 0.14 0.03 1574 3 123 "by submitter,freq,cluster" Benign 0.246 5 Tolerant 0.54 2.75 339 moderately conservative 605622 5q31 protocadherin 12 714 rs164075 PCDH12 51294 5 141316448 NM_016580 NP_057664 A/C H385N minus 24667595 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.4 0.37 0.03 140 2 0.14 0.03 1574 3 123 "by submitter,freq,cluster" Benign 0.246 5 Tolerant 0.54 2.75 339 moderately conservative 605622 5q31 protocadherin 12 715 rs164515 PCDH12 51294 5 141315682 NM_016580 NP_057664 A/G S640N minus 24621926 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.25 0.25 0 48 1 0.12 0.03 1586 3 123 "by doubleHit,submitter,freq,cluster" Benign 0.272 5 Tolerant 0.21 2.75 331 conservative 605622 5q31 protocadherin 12 716 rs165815 ARVCF 421 22 18334027 NM_001670 NP_001661 C/T R906Q plus 481084 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 24 0.08 0.12 0.05 374 5 0.44 0.02 138 4 123 "HapMap,doubleHit,freq,cluster" Benign 0.098 15 Borderline 0.16 2.99 34 conservative 602269 22q11.21 armadillo repeat gene deletes in velocardiofacial syndrome 717 rs165815 ARVCF 421 22 18334027 NM_001670 NP_001661 C/T R906Q plus 481084 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 90 0.12 0.12 0.05 374 5 0.44 0.02 138 4 123 "HapMap,doubleHit,freq,cluster" Benign 0.098 15 Borderline 0.16 2.99 34 conservative 602269 22q11.21 armadillo repeat gene deletes in velocardiofacial syndrome 718 rs165815 ARVCF 421 22 18334027 NM_001670 NP_001661 C/T R906Q plus 8287556 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.12 0.12 0.05 374 5 0.44 0.02 138 4 123 "HapMap,doubleHit,freq,cluster" Benign 0.098 15 Borderline 0.16 2.99 34 conservative 602269 22q11.21 armadillo repeat gene deletes in velocardiofacial syndrome 719 rs165815 ARVCF 421 22 18334027 NM_001670 NP_001661 C/T R906Q plus 8287556 1303 SEQUENOM CEPH CEPH (92) 92 0.07 0.12 0.05 374 5 0.44 0.02 138 4 123 "HapMap,doubleHit,freq,cluster" Benign 0.098 15 Borderline 0.16 2.99 34 conservative 602269 22q11.21 armadillo repeat gene deletes in velocardiofacial syndrome 720 rs165815 ARVCF 421 22 18334027 NM_001670 NP_001661 C/T R906Q plus 23789050 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.23 0.12 0.05 374 5 0.44 0.02 138 4 123 "HapMap,doubleHit,freq,cluster" Benign 0.098 15 Borderline 0.16 2.99 34 conservative 602269 22q11.21 armadillo repeat gene deletes in velocardiofacial syndrome 721 rs167479 RGL3 57139 19 11387765 XM_290867 XP_290867 A/C P162H minus 1937759 1303 SEQUENOM CEPH CEPH (92) 92 0.14 0.16 0.12 98 2 0.28 0.06 44 2 121 "by doubleHit,freq,cluster" Intolerant 0.02 2.9 21 moderately conservative 19p13.2 ral guanine nucleotide dissociation stimulator-like 3 722 rs167479 RGL3 57139 19 11387765 XM_290867 XP_290867 A/C P162H minus 1937780 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 6 0.5 0.16 0.12 98 2 0.28 0.06 44 2 121 "by doubleHit,freq,cluster" Intolerant 0.02 2.9 21 moderately conservative 19p13.2 ral guanine nucleotide dissociation stimulator-like 3 723 rs169068 SSTR5 6755 16 1069873 NM_001053 NP_001044 C/T P335L plus 3173187 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 36 0.39 0.39 0 36 1 0.16 0 1488 1 113 "by doubleHit,freq,cluster" Possibly damaging 1.87 20 Borderline 0.14 2.92 27 moderately conservative 182455 16p13.3 somatostatin receptor 5 724 rs169547 BRCA2 675 13 31827387 NM_000059 NP_000050 A/G V2466A minus 16355878 693 EGP_SNPS PDR90 NIHPDR 148 0.03 0.03 0.01 266 2 0.01 0.01 248 2 121 "HapMap,freq,cluster" moderately conservative 600185 13q12.3 "breast cancer 2, early onset" 725 rs169547 BRCA2 675 13 31827387 NM_000059 NP_000050 A/G V2466A minus 16355878 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.02 0.03 0.01 266 2 0.01 0.01 248 2 121 "HapMap,freq,cluster" moderately conservative 600185 13q12.3 "breast cancer 2, early onset" 726 rs172562 TBX18 9096 6 85530477 XM_496819 XP_496819 C/T G48R plus 1746987 1303 SEQUENOM CEPH CEPH (92) 92 0.38 0.38 0 92 1 120 "by doubleHit,freq,cluster" moderately radical 604613 6q14-q15 T-box 18 727 rs180749 AGXT2 64902 5 35069362 NM_031900 NP_114106 A/G T212I plus 626437 1303 SEQUENOM CEPH CEPH (92) 92 0.01 0.01 0 92 1 0.2 0.01 1572 3 123 "by doubleHit,freq,cluster" Benign 0.247 8 Tolerant 0.53 2.77 36 moderately conservative 5p13 alanine-glyoxylate aminotransferase 2 728 rs181206 IL27 246778 16 28420904 NM_145659 NP_663634 C/T L119P minus 617395 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.29 0.36 0.08 198 3 0.09 0.06 48 2 87 by freq moderately conservative 608273 16p11 interleukin 27 729 rs181206 IL27 246778 16 28420904 NM_145659 NP_663634 C/T L119P minus 617395 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 92 0.3 0.36 0.08 198 3 0.09 0.06 48 2 87 by freq moderately conservative 608273 16p11 interleukin 27 730 rs181206 IL27 246778 16 28420904 NM_145659 NP_663634 C/T L119P minus 1971619 1303 SEQUENOM CEPH CEPH (92) 92 0.43 0.36 0.08 198 3 0.09 0.06 48 2 87 by freq moderately conservative 608273 16p11 interleukin 27 731 rs185819 TNXB 7148 6 32158045 NM_019105 NP_061978 C/T H1248R plus 80760 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 83 0.13 0.3 0.16 223 3 0.38 0.06 260 4 123 "by doubleHit,freq,cluster" Tolerant 1 2.85 16 conservative 600985 6p21.3 tenascin XB 732 rs185819 TNXB 7148 6 32158045 NM_019105 NP_061978 C/T H1248R plus 7852581 1303 SEQUENOM CEPH CEPH (92) 92 0.38 0.3 0.16 223 3 0.38 0.06 260 4 123 "by doubleHit,freq,cluster" Tolerant 1 2.85 16 conservative 600985 6p21.3 tenascin XB 733 rs185819 TNXB 7148 6 32158045 NM_019105 NP_061978 C/T H1248R plus 24308158 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.44 0.3 0.16 223 3 0.38 0.06 260 4 123 "by doubleHit,freq,cluster" Tolerant 1 2.85 16 conservative 600985 6p21.3 tenascin XB 734 rs188703 CSPG2 1462 5 82870055 NM_004385 NP_004376 C/T R1826H minus 648869 1303 SEQUENOM CEPH CEPH (92) 92 0.44 0.44 0 92 1 121 "by doubleHit,submitter,freq,cluster" Benign 0.626 5 Borderline 0.13 2.95 9 conservative 118661 5q14.3 chondroitin sulfate proteoglycan 2 (versican) 735 rs194520 STEAP2 261729 7 89499097 NM_152999 NP_694544 G/T F17C plus 256300 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 83 0.4 0.44 0.07 143 2 0.2 0.14 166 2 79 "HapMap,freq" radical 605094 7q21 six transmembrane epithelial antigen of prostate 2 736 rs194520 STEAP2 261729 7 89499097 NM_152999 NP_694544 G/T F17C plus 256300 885 TSC-CSHL HapMap-CEPH-30-trios 60 0.5 0.44 0.07 143 2 0.2 0.14 166 2 79 "HapMap,freq" radical 605094 7q21 six transmembrane epithelial antigen of prostate 2 737 rs194524 STEAP2 261729 7 89506483 NM_152999 NP_694544 A/G R456Q plus 256305 885 TSC-CSHL HapMap-CEPH-30-trios 60 0.5 0.5 0 84 2 0.28 0.08 92 2 123 "HapMap,freq" Potentially damaging 1.415 6 conservative 605094 7q21 six transmembrane epithelial antigen of prostate 2 738 rs194524 STEAP2 261729 7 89506483 NM_152999 NP_694544 A/G R456Q plus 24680669 1371 PERLEGEN AFD_EUR_PANEL European American (24) 24 0.5 0.5 0 84 2 0.28 0.08 92 2 123 "HapMap,freq" Potentially damaging 1.415 6 conservative 605094 7q21 six transmembrane epithelial antigen of prostate 2 739 rs194525 STEAP2 261729 7 89506541 NM_152999 NP_694544 G/T M475I plus 14567838 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.13 0.13 0 120 1 121 "HapMap,doubleHit,freq,cluster" conservative 605094 7q21 six transmembrane epithelial antigen of prostate 2 740 rs198977 KLK2 3817 19 56073589 NM_005551 NP_005542 C/T R250W plus 2041639 1303 SEQUENOM CEPH CEPH (92) 92 0.24 0.24 0 92 1 0.25 0 1498 1 106 "by cluster,freq" Possibly damaging 1.823 77 Borderline 0.18 2.78 71 moderately radical 147960 19q13.41 "kallikrein 2, prostatic" 741 rs202676 FOLH1 2346 11 49184196 NM_004476 NP_004467 C/T Y75H minus 605502 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.14 0.19 0.04 62 2 0.4 0.07 140 4 123 "by doubleHit,freq,cluster" Possibly damaging 1.528 9 Tolerant 0.36 2.83 16 moderately conservative 600934 11p11.2 folate hydrolase (prostate-specific membrane antigen) 1 742 rs202676 FOLH1 2346 11 49184196 NM_004476 NP_004467 C/T Y75H minus 23739871 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.19 0.04 62 2 0.4 0.07 140 4 123 "by doubleHit,freq,cluster" Possibly damaging 1.528 9 Tolerant 0.36 2.83 16 moderately conservative 600934 11p11.2 folate hydrolase (prostate-specific membrane antigen) 1 743 rs203462 AKAP10 11216 17 19753133 NM_007202 NP_009133 A/G I646V minus 266958 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.07 0.42 0.12 202 4 0.27 0.14 142 4 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.62 9 conservative 604694 17p11.1 A kinase (PRKA) anchor protein 10 744 rs203462 AKAP10 11216 17 19753133 NM_007202 NP_009133 A/G I646V minus 1647656 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.41 0.42 0.12 202 4 0.27 0.14 142 4 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.62 9 conservative 604694 17p11.1 A kinase (PRKA) anchor protein 10 745 rs203462 AKAP10 11216 17 19753133 NM_007202 NP_009133 A/G I646V minus 1647656 1303 SEQUENOM CEPH CEPH (92) 46 0.5 0.42 0.12 202 4 0.27 0.14 142 4 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.62 9 conservative 604694 17p11.1 A kinase (PRKA) anchor protein 10 746 rs203462 AKAP10 11216 17 19753133 NM_007202 NP_009133 A/G I646V minus 24590791 1371 PERLEGEN AFD_EUR_PANEL European American (24) 24 0.5 0.42 0.12 202 4 0.27 0.14 142 4 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.62 9 conservative 604694 17p11.1 A kinase (PRKA) anchor protein 10 747 rs203710 PVR 5817 19 49853878 NM_006505 NP_006496 A/G I340M plus 484460 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.07 0.02 0.01 226 3 121 "HapMap,freq,cluster" Benign 0.946 9 conservative 173850 19q13.2 poliovirus receptor 748 rs203710 PVR 5817 19 49853878 NM_006505 NP_006496 A/G I340M plus 484460 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 94 0.02 0.02 0.01 226 3 121 "HapMap,freq,cluster" Benign 0.946 9 conservative 173850 19q13.2 poliovirus receptor 749 rs203710 PVR 5817 19 49853878 NM_006505 NP_006496 A/G I340M plus 1821115 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.02 0.02 0.01 226 3 121 "HapMap,freq,cluster" Benign 0.946 9 conservative 173850 19q13.2 poliovirus receptor 750 rs204896 TNXB 7148 6 32172076 NM_019105 NP_061978 C/T R511H plus 661712 1303 SEQUENOM CEPH CEPH (92) 92 0.07 0.07 0.01 140 2 0.11 0.02 1582 3 123 "by cluster,freq" Potentially intolerant 0.09 2.92 14 conservative 600985 6p21.3 tenascin XB 751 rs204896 TNXB 7148 6 32172076 NM_019105 NP_061978 C/T R511H plus 23714822 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.07 0.01 140 2 0.11 0.02 1582 3 123 "by cluster,freq" Potentially intolerant 0.09 2.92 14 conservative 600985 6p21.3 tenascin XB 752 rs204900 TNXB 7148 6 32164558 NM_019105 NP_061978 G/T S873A minus 268677 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 83 0.06 0.11 0.07 175 2 0.18 0 83 1 121 "by doubleHit,freq,cluster" Intolerant 0.05 2.8 17 moderately conservative 600985 6p21.3 tenascin XB 753 rs204900 TNXB 7148 6 32164558 NM_019105 NP_061978 G/T S873A minus 466452 1303 SEQUENOM CEPH CEPH (92) 92 0.16 0.11 0.07 175 2 0.18 0 83 1 121 "by doubleHit,freq,cluster" Intolerant 0.05 2.8 17 moderately conservative 600985 6p21.3 tenascin XB 754 rs205498 TRIM25 7706 17 52333793 NM_005082 NP_005073 C/T P358L minus 1830958 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.28 0.28 0 120 1 0.2 0 1490 1 121 "HapMap,doubleHit,freq,cluster" moderately conservative 600453 17q23.1 tripartite motif-containing 25 755 rs208696 SASH1 23328 6 148906950 NM_015278 NP_056093 A/G Q884R plus 5221682 1303 SEQUENOM CEPH CEPH (92) 92 0.01 0.16 0.29 140 2 0.39 0.06 1586 3 123 "by doubleHit,freq,cluster" Benign 0.084 5 conservative 607955 6q24.3 SAM and SH3 domain containing 1 756 rs208696 SASH1 23328 6 148906950 NM_015278 NP_056093 A/G Q884R plus 24484549 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.44 0.16 0.29 140 2 0.39 0.06 1586 3 123 "by doubleHit,freq,cluster" Benign 0.084 5 conservative 607955 6q24.3 SAM and SH3 domain containing 1 757 rs208753 PCM1 5108 8 17859195 NM_006197 NP_006188 A/G M597V plus 1846412 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.26 0.26 0 260 3 0.29 0.04 1558 3 123 "HapMap,submitter,freq,cluster" Possibly damaging 1.882 5 conservative 600299 8p22-p21.3 pericentriolar material 1 758 rs208753 PCM1 5108 8 17859195 NM_006197 NP_006188 A/G M597V plus 1846412 1303 SEQUENOM CEPH CEPH (92) 92 0.26 0.26 0 260 3 0.29 0.04 1558 3 123 "HapMap,submitter,freq,cluster" Possibly damaging 1.882 5 conservative 600299 8p22-p21.3 pericentriolar material 1 759 rs208753 PCM1 5108 8 17859195 NM_006197 NP_006188 A/G M597V plus 24664200 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.25 0.26 0 260 3 0.29 0.04 1558 3 123 "HapMap,submitter,freq,cluster" Possibly damaging 1.882 5 conservative 600299 8p22-p21.3 pericentriolar material 1 760 rs210280 ZNF11B 7558 10 42409971 NM_006955 NP_008886 A/G R145C plus 2677121 1303 SEQUENOM CEPH CEPH (92) 92 0.26 0.26 0 92 1 122 "by doubleHit,freq,cluster" Probably damaging 2.631 7 Borderline 0.19 2.76 27 radical 194522 10q11.2 zinc finger protein 11b (KOX 2) 761 rs213950 CFTR 1080 7 116793484 NM_000492 NP_000483 A/G V470M plus 24012792 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.44 0.44 0 48 1 0.3 0.26 94 2 123 "by doubleHit,submitter,freq,cluster" Potentially damaging 1.258 29 conservative 602421 7q31.2 "cystic fibrosis transmembrane conductance regulator, ATP-binding cassette (sub-family C, member 7)" 762 rs216321 VWF 7450 12 6014245 NM_000552 NP_000543 C/T Q852R plus 667776 1303 SEQUENOM CEPH CEPH (92) 92 0.05 0.07 0.03 140 2 0.19 0.01 1590 3 123 "by submitter,freq,cluster" Potentially damaging 1.357 10 conservative 193400 12p13.3 von Willebrand factor 763 rs216321 VWF 7450 12 6014245 NM_000552 NP_000543 C/T Q852R plus 24166811 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.07 0.03 140 2 0.19 0.01 1590 3 123 "by submitter,freq,cluster" Potentially damaging 1.357 10 conservative 193400 12p13.3 von Willebrand factor 764 rs217086 CTSC 1075 11 87685231 NM_001814 NP_001805 A/G I153T plus 745848 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 10 0.4 0.18 0.15 56 2 0.25 0.1 66 2 123 "by doubleHit,freq,cluster" Borderline 1.041 14 moderately conservative 602365 11q14.1-q14.3 cathepsin C 765 rs217086 CTSC 1075 11 87685231 NM_001814 NP_001805 A/G I153T plus 23377436 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.13 0.18 0.15 56 2 0.25 0.1 66 2 123 "by doubleHit,freq,cluster" Borderline 1.041 14 moderately conservative 602365 11q14.1-q14.3 cathepsin C 766 rs217180 PMFBP1 83449 16 70742130 NM_031293 NP_112583 A/G A172T minus 3288372 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.08 0.15 0.09 260 3 0.12 0.04 94 2 123 "HapMap,submitter,freq" moderately conservative 16q22.2 polyamine modulated factor 1 binding protein 1 767 rs217180 PMFBP1 83449 16 70742130 NM_031293 NP_112583 A/G A172T minus 3288372 1303 SEQUENOM CEPH CEPH (92) 92 0.25 0.15 0.09 260 3 0.12 0.04 94 2 123 "HapMap,submitter,freq" moderately conservative 16q22.2 polyamine modulated factor 1 binding protein 1 768 rs217180 PMFBP1 83449 16 70742130 NM_031293 NP_112583 A/G A172T minus 24576958 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.15 0.09 260 3 0.12 0.04 94 2 123 "HapMap,submitter,freq" moderately conservative 16q22.2 polyamine modulated factor 1 binding protein 1 769 rs220379 ZNF263 10127 16 3279436 NM_005741 NP_005732 C/G C310S plus 595513 1303 SEQUENOM CEPH CEPH (92) 92 0.42 0.42 0 92 1 116 "by doubleHit,freq,cluster" Tolerant 0.8 2.8 19 moderately radical 604191 16p13.3 zinc finger protein 263 770 rs220461 GSG2 83903 17 3574961 NM_031965 NP_114171 A/G I328T minus 1629759 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.27 0.25 0.06 260 3 0.37 0.06 1592 3 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 17p13 haspin 771 rs220461 GSG2 83903 17 3574961 NM_031965 NP_114171 A/G I328T minus 1629759 1303 SEQUENOM CEPH CEPH (92) 92 0.19 0.25 0.06 260 3 0.37 0.06 1592 3 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 17p13 haspin 772 rs220461 GSG2 83903 17 3574961 NM_031965 NP_114171 A/G I328T minus 24443575 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.33 0.25 0.06 260 3 0.37 0.06 1592 3 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 17p13 haspin 773 rs220462 GSG2 83903 17 3574589 NM_031965 NP_114171 C/T G204D minus 1629760 1303 SEQUENOM CEPH CEPH (92) 92 0.46 0.46 0 92 1 121 "by doubleHit,freq" moderately conservative 17p13 haspin 774 rs220479 ITGAE 3682 17 3603924 NM_002208 NP_002199 A/G I477V minus 21431179 1303 SEQUENOM CEPH CEPH (92) 92 0.29 0.29 0 92 1 121 "by cluster,freq" Benign 0.62 6 conservative 604682 17p13 "integrin, alpha E (antigen CD103, human mucosal lymphocyte antigen 1; alpha polypeptide)" 775 rs224331 GDF5 8200 20 33485801 NM_000557 NP_000548 A/C S276A plus 8375421 1303 SEQUENOM CEPH CEPH (92) 92 0.37 0.37 0 138 2 0.36 0.17 92 2 123 "by doubleHit,freq,cluster" Tolerant 0.4 2.79 81 moderately conservative 601146 20q11.2 growth differentiation factor 5 (cartilage-derived morphogenetic protein-1) 776 rs224331 GDF5 8200 20 33485801 NM_000557 NP_000548 A/C S276A plus 23566430 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.37 0.37 0 138 2 0.36 0.17 92 2 123 "by doubleHit,freq,cluster" Tolerant 0.4 2.79 81 moderately conservative 601146 20q11.2 growth differentiation factor 5 (cartilage-derived morphogenetic protein-1) 777 rs226794 ADAMTS5 11096 21 27224226 NM_007038 NP_008969 A/G L692P plus 2775282 1303 SEQUENOM CEPH CEPH (92) 92 0.2 0.14 0.09 159 3 0.28 0.29 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.899 7 moderately conservative 605007 21q21.3 "a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2)" 778 rs226794 ADAMTS5 11096 21 27224226 NM_007038 NP_008969 A/G L692P plus 4008063 634 PERLEGEN NCBI|NIHPDR NIHPDR 19 0.11 0.14 0.09 159 3 0.28 0.29 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.899 7 moderately conservative 605007 21q21.3 "a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2)" 779 rs226794 ADAMTS5 11096 21 27224226 NM_007038 NP_008969 A/G L692P plus 24025516 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.14 0.09 159 3 0.28 0.29 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.899 7 moderately conservative 605007 21q21.3 "a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2)" 780 rs228942 IL2RB 3560 22 35849119 NM_000878 NP_000869 A/C D391E minus 4479476 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 42 0.17 0.19 0.03 254 3 0.24 0.04 1548 2 120 "HapMap,doubleHit,freq,cluster" Benign 0.114 5 conservative 146710 22q13.1 "interleukin 2 receptor, beta" 781 rs228942 IL2RB 3560 22 35849119 NM_000878 NP_000869 A/C D391E minus 4479476 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.17 0.19 0.03 254 3 0.24 0.04 1548 2 120 "HapMap,doubleHit,freq,cluster" Benign 0.114 5 conservative 146710 22q13.1 "interleukin 2 receptor, beta" 782 rs228942 IL2RB 3560 22 35849119 NM_000878 NP_000869 A/C D391E minus 4479476 1303 SEQUENOM CEPH CEPH (92) 92 0.22 0.19 0.03 254 3 0.24 0.04 1548 2 120 "HapMap,doubleHit,freq,cluster" Benign 0.114 5 conservative 146710 22q13.1 "interleukin 2 receptor, beta" 783 rs229150 SCFD1 23256 14 30169489 NM_016106 NP_057190 C/T K63R minus 24542261 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.35 0.35 0 48 1 0.27 0.04 94 2 123 "by doubleHit,submitter,freq,cluster" Benign 0.325 11 Tolerant 0.31 2.82 15 conservative 14q12 sec1 family domain containing 1 784 rs231775 CTLA4 1493 2 204558220 NM_005214 NP_005205 A/G T17A plus 545243 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.07 0.3 0.09 254 4 0.27 0.06 1676 7 123 "by doubleHit,submitter,freq,cluster" Borderline 1.016 18 moderately conservative 123890 2q33 cytotoxic T-lymphocyte-associated protein 4 785 rs231775 CTLA4 1493 2 204558220 NM_005214 NP_005205 A/G T17A plus 545243 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 90 0.37 0.3 0.09 254 4 0.27 0.06 1676 7 123 "by doubleHit,submitter,freq,cluster" Borderline 1.016 18 moderately conservative 123890 2q33 cytotoxic T-lymphocyte-associated protein 4 786 rs231775 CTLA4 1493 2 204558220 NM_005214 NP_005205 A/G T17A plus 6903722 775 SNP500CANCER CAUC1 Caucasian (31) 58 0.21 0.3 0.09 254 4 0.27 0.06 1676 7 123 "by doubleHit,submitter,freq,cluster" Borderline 1.016 18 moderately conservative 123890 2q33 cytotoxic T-lymphocyte-associated protein 4 787 rs231775 CTLA4 1493 2 204558220 NM_005214 NP_005205 A/G T17A plus 6903722 1303 SEQUENOM CEPH CEPH (92) 92 0.31 0.3 0.09 254 4 0.27 0.06 1676 7 123 "by doubleHit,submitter,freq,cluster" Borderline 1.016 18 moderately conservative 123890 2q33 cytotoxic T-lymphocyte-associated protein 4 788 rs232518 NCAM2 4685 21 21668058 NM_004540 NP_004531 C/T L350P plus 2257786 782 TSC-CSHL WICGR6_CAUCASIAN_POOLED WICGR Caucasian (48) 96 0.32 0.27 0.05 254 4 0.45 0.01 1662 4 123 "by doubleHit,submitter,freq,cluster" Probably damaging 2.383 7 Tolerant 0.3 2.82 32 moderately conservative 602040 21q21.1 neural cell adhesion molecule 2 789 rs232518 NCAM2 4685 21 21668058 NM_004540 NP_004531 C/T L350P plus 2257786 1303 SEQUENOM CEPH CEPH (92) 92 0.25 0.27 0.05 254 4 0.45 0.01 1662 4 123 "by doubleHit,submitter,freq,cluster" Probably damaging 2.383 7 Tolerant 0.3 2.82 32 moderately conservative 602040 21q21.1 neural cell adhesion molecule 2 790 rs232518 NCAM2 4685 21 21668058 NM_004540 NP_004531 C/T L350P plus 4002906 634 PERLEGEN NCBI|NIHPDR NIHPDR 18 0.22 0.27 0.05 254 4 0.45 0.01 1662 4 123 "by doubleHit,submitter,freq,cluster" Probably damaging 2.383 7 Tolerant 0.3 2.82 32 moderately conservative 602040 21q21.1 neural cell adhesion molecule 2 791 rs232518 NCAM2 4685 21 21668058 NM_004540 NP_004531 C/T L350P plus 24209420 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.27 0.05 254 4 0.45 0.01 1662 4 123 "by doubleHit,submitter,freq,cluster" Probably damaging 2.383 7 Tolerant 0.3 2.82 32 moderately conservative 602040 21q21.1 neural cell adhesion molecule 2 792 rs233223 MEP1B 4225 18 28049099 NM_005925 NP_005916 A/G S546P minus 557201 1303 SEQUENOM CEPH CEPH (92) 92 0.12 0.12 0 92 1 120 "by doubleHit,cluster" Possibly damaging 1.74 7 moderately conservative 600389 18q12.2-q12.3 "meprin A, beta" 793 rs235768 BMP2 650 20 6707115 NM_001200 NP_001191 A/T R190S plus 304296 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 7 0.5 0.32 0.08 239 4 0.21 0.06 48 2 121 "by doubleHit,freq,cluster" Probably damaging 2.152 60 Intolerant 0.01 2.83 81 moderately radical 112261 20p12 bone morphogenetic protein 2 794 rs235768 BMP2 650 20 6707115 NM_001200 NP_001191 A/T R190S plus 304296 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 90 0.39 0.32 0.08 239 4 0.21 0.06 48 2 121 "by doubleHit,freq,cluster" Probably damaging 2.152 60 Intolerant 0.01 2.83 81 moderately radical 112261 20p12 bone morphogenetic protein 2 795 rs235768 BMP2 650 20 6707115 NM_001200 NP_001191 A/T R190S plus 3176830 619 WICVAR MITOGPOP6 CORIELL Mixed 50 0.22 0.32 0.08 239 4 0.21 0.06 48 2 121 "by doubleHit,freq,cluster" Probably damaging 2.152 60 Intolerant 0.01 2.83 81 moderately radical 112261 20p12 bone morphogenetic protein 2 796 rs235768 BMP2 650 20 6707115 NM_001200 NP_001191 A/T R190S plus 8367997 1303 SEQUENOM CEPH CEPH (92) 92 0.29 0.32 0.08 239 4 0.21 0.06 48 2 121 "by doubleHit,freq,cluster" Probably damaging 2.152 60 Intolerant 0.01 2.83 81 moderately radical 112261 20p12 bone morphogenetic protein 2 797 rs237831 DDX28 55794 16 66614597 NM_018380 NP_060850 A/G T4A minus 129227 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 78 0.14 0.11 0.04 304 4 121 "HapMap,freq" moderately conservative 607618 16q22.1 DEAD (Asp-Glu-Ala-Asp) box polypeptide 28 798 rs237831 DDX28 55794 16 66614597 NM_018380 NP_060850 A/G T4A minus 129227 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.07 0.11 0.04 304 4 121 "HapMap,freq" moderately conservative 607618 16q22.1 DEAD (Asp-Glu-Ala-Asp) box polypeptide 28 799 rs237831 DDX28 55794 16 66614597 NM_018380 NP_060850 A/G T4A minus 129227 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.07 0.11 0.04 304 4 121 "HapMap,freq" moderately conservative 607618 16q22.1 DEAD (Asp-Glu-Ala-Asp) box polypeptide 28 800 rs237831 DDX28 55794 16 66614597 NM_018380 NP_060850 A/G T4A minus 129227 1303 SEQUENOM CEPH CEPH (92) 92 0.14 0.11 0.04 304 4 121 "HapMap,freq" moderately conservative 607618 16q22.1 DEAD (Asp-Glu-Ala-Asp) box polypeptide 28 801 rs238234 CAMTA2 23125 17 4824542 NM_015099 NP_055914 C/G A267P plus 129424 1303 SEQUENOM CEPH CEPH (92) 92 0.26 0.26 0 92 1 121 "by doubleHit,freq,cluster" conservative 17p13.3 calmodulin binding transcription activator 2 802 rs240768 HELIC1 10973 6 101064065 NM_006828 NP_006819 C/T Y2176C plus 1631964 1303 SEQUENOM CEPH CEPH (92) 92 0.02 0.04 0.05 164 3 0.12 0.03 1658 6 123 "by doubleHit,submitter,freq,cluster" Potentially intolerant 0.07 2.89 16 radical 6q16 "helicase, ATP binding 1" 803 rs240768 HELIC1 10973 6 101064065 NM_006828 NP_006819 C/T Y2176C plus 16335969 902 AFFY Caucasian 24 0.13 0.04 0.05 164 3 0.12 0.03 1658 6 123 "by doubleHit,submitter,freq,cluster" Potentially intolerant 0.07 2.89 16 radical 6q16 "helicase, ATP binding 1" 804 rs240768 HELIC1 10973 6 101064065 NM_006828 NP_006819 C/T Y2176C plus 23407849 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.04 0.05 164 3 0.12 0.03 1658 6 123 "by doubleHit,submitter,freq,cluster" Potentially intolerant 0.07 2.89 16 radical 6q16 "helicase, ATP binding 1" 805 rs240780 HELIC1 10973 6 101070868 NM_006828 NP_006819 C/G S1995C plus 1631950 1303 SEQUENOM CEPH CEPH (92) 92 0.34 0.38 0.08 140 2 0.21 0.09 92 2 123 "by doubleHit,submitter,freq,cluster" Probably damaging 2.068 6 Intolerant 0.03 2.77 20 moderately radical 6q16 "helicase, ATP binding 1" 806 rs240780 HELIC1 10973 6 101070868 NM_006828 NP_006819 C/G S1995C plus 24425049 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.46 0.38 0.08 140 2 0.21 0.09 92 2 123 "by doubleHit,submitter,freq,cluster" Probably damaging 2.068 6 Intolerant 0.03 2.77 20 moderately radical 6q16 "helicase, ATP binding 1" 807 rs241447 TAP2 6891 6 32904729 NM_000544 NP_000535 A/G T665A minus 1954321 1303 SEQUENOM CEPH CEPH (92) 92 0.13 0.22 0.07 326 3 0.35 0 1474 1 123 "by doubleHit,freq,cluster" Benign 0.502 20 moderately conservative 170261 6p21.3 "transporter 2, ATP-binding cassette, sub-family B (MDR/TAP)" 808 rs241447 TAP2 6891 6 32904729 NM_000544 NP_000535 A/G T665A minus 3173073 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 50 0.22 0.22 0.07 326 3 0.35 0 1474 1 123 "by doubleHit,freq,cluster" Benign 0.502 20 moderately conservative 170261 6p21.3 "transporter 2, ATP-binding cassette, sub-family B (MDR/TAP)" 809 rs241447 TAP2 6891 6 32904729 NM_000544 NP_000535 A/G T665A minus 24796293 1303 SEQUENOM CEPH CEPH (92) 184 0.27 0.22 0.07 326 3 0.35 0 1474 1 123 "by doubleHit,freq,cluster" Benign 0.502 20 moderately conservative 170261 6p21.3 "transporter 2, ATP-binding cassette, sub-family B (MDR/TAP)" 810 rs241448 TAP2 6891 6 32904663 NM_000544 NP_000535 C/T STOP687Q minus 1954322 1303 SEQUENOM CEPH CEPH (92) 92 0.3 0.26 0.07 140 2 120 "by doubleHit,freq,cluster" Probably damaging Intolerant radical 170261 6p21.3 "transporter 2, ATP-binding cassette, sub-family B (MDR/TAP)" 811 rs241448 TAP2 6891 6 32904663 NM_000544 NP_000535 C/T STOP687Q minus 3173074 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 48 0.19 0.26 0.07 140 2 120 "by doubleHit,freq,cluster" Probably damaging Intolerant radical 170261 6p21.3 "transporter 2, ATP-binding cassette, sub-family B (MDR/TAP)" 812 rs244903 RARS 5917 5 167846088 NM_002887 NP_002878 A/G V3I plus 818727 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.29 0.44 0.05 364 5 0.1 0.01 1616 4 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.004 8 conservative 107820 5q35.1 arginyl-tRNA synthetase 813 rs244903 RARS 5917 5 167846088 NM_002887 NP_002878 A/G V3I plus 818727 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 90 0.44 0.44 0.05 364 5 0.1 0.01 1616 4 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.004 8 conservative 107820 5q35.1 arginyl-tRNA synthetase 814 rs244903 RARS 5917 5 167846088 NM_002887 NP_002878 A/G V3I plus 2274905 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.49 0.44 0.05 364 5 0.1 0.01 1616 4 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.004 8 conservative 107820 5q35.1 arginyl-tRNA synthetase 815 rs244903 RARS 5917 5 167846088 NM_002887 NP_002878 A/G V3I plus 2274905 1303 SEQUENOM CEPH CEPH (92) 92 0.42 0.44 0.05 364 5 0.1 0.01 1616 4 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.004 8 conservative 107820 5q35.1 arginyl-tRNA synthetase 816 rs244903 RARS 5917 5 167846088 NM_002887 NP_002878 A/G V3I plus 24671348 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.42 0.44 0.05 364 5 0.1 0.01 1616 4 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.004 8 conservative 107820 5q35.1 arginyl-tRNA synthetase 817 rs246669 PCDHB4 56131 5 140483421 NM_018938 NP_061761 C/T T553A minus 24811105 1303 SEQUENOM CEPH CEPH (92) 184 0.18 0.18 0 184 1 123 by freq Borderline 1.218 103 Tolerant 0.48 2.77 130 moderately conservative 606330 5q31 protocadherin beta 4 818 rs246679 PCDHB1 29930 5 140413573 NM_013340 NP_037472 C/G F778L minus 521335 1303 SEQUENOM CEPH CEPH (92) 92 0.03 0.03 0 92 1 98 by freq Tolerant 1 2.77 95 conservative 606327 5q31 protocadherin beta 1 819 rs246703 PCDHB6 56130 5 140511930 NM_018939 NP_061762 C/G H636Q minus 1652768 1303 SEQUENOM CEPH CEPH (92) 92 0.46 0.46 0 92 1 121 by freq Borderline 1.205 104 Tolerant 1 2.77 130 conservative 606332 5q31 protocadherin beta 6 820 rs259028 ZFYVE16 9765 5 79770053 NM_014733 NP_055548 C/T I598T plus 2228689 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 76 0.05 0.03 0.01 334 4 0.21 0.1 222 4 123 "HapMap,submitter,freq,cluster" Possibly damaging 1.711 5 moderately conservative 608880 5p15.2-q14.3 "zinc finger, FYVE domain containing 16" 821 rs259028 ZFYVE16 9765 5 79770053 NM_014733 NP_055548 C/T I598T plus 2228689 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.03 0.03 0.01 334 4 0.21 0.1 222 4 123 "HapMap,submitter,freq,cluster" Possibly damaging 1.711 5 moderately conservative 608880 5p15.2-q14.3 "zinc finger, FYVE domain containing 16" 822 rs259028 ZFYVE16 9765 5 79770053 NM_014733 NP_055548 C/T I598T plus 2228689 1303 SEQUENOM CEPH CEPH (92) 92 0.03 0.03 0.01 334 4 0.21 0.1 222 4 123 "HapMap,submitter,freq,cluster" Possibly damaging 1.711 5 moderately conservative 608880 5p15.2-q14.3 "zinc finger, FYVE domain containing 16" 823 rs259028 ZFYVE16 9765 5 79770053 NM_014733 NP_055548 C/T I598T plus 23399732 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.03 0.01 334 4 0.21 0.1 222 4 123 "HapMap,submitter,freq,cluster" Possibly damaging 1.711 5 moderately conservative 608880 5p15.2-q14.3 "zinc finger, FYVE domain containing 16" 824 rs260462 ZNF544 27300 19 63465883 NM_014480 NP_055295 A/G Q700R plus 540180 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 8 0.38 0.46 0.03 308 5 0.41 0.01 1638 5 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 19q13.43 zinc finger protein 544 825 rs260462 ZNF544 27300 19 63465883 NM_014480 NP_055295 A/G Q700R plus 540180 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 46 0.5 0.46 0.03 308 5 0.41 0.01 1638 5 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 19q13.43 zinc finger protein 544 826 rs260462 ZNF544 27300 19 63465883 NM_014480 NP_055295 A/G Q700R plus 540180 885 TSC-CSHL HapMap-CEPH-30-trios 114 0.45 0.46 0.03 308 5 0.41 0.01 1638 5 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 19q13.43 zinc finger protein 544 827 rs260462 ZNF544 27300 19 63465883 NM_014480 NP_055295 A/G Q700R plus 540180 1303 SEQUENOM CEPH CEPH (92) 92 0.44 0.46 0.03 308 5 0.41 0.01 1638 5 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 19q13.43 zinc finger protein 544 828 rs260462 ZNF544 27300 19 63465883 NM_014480 NP_055295 A/G Q700R plus 24536462 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.48 0.46 0.03 308 5 0.41 0.01 1638 5 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 19q13.43 zinc finger protein 544 829 rs266880 KLK3 354 19 56050283 NM_145864 NP_665863 C/G P87R plus 2041378 1303 SEQUENOM CEPH CEPH (92) 92 0.45 0.45 0 92 1 0.2 0 1494 1 120 "by doubleHit,freq,cluster" moderately radical 176820 19q13.41 "kallikrein 3, (prostate specific antigen)" 830 rs267561 ITGA9 3680 3 37549955 NM_002207 NP_002198 C/T G507E minus 1490039 1303 SEQUENOM CEPH CEPH (92) 92 0.49 0.47 0.03 140 2 0.29 0.21 71 2 123 "by doubleHit,submitter,freq,cluster" Tolerant 0.35 2.82 16 moderately conservative 603963 3p21.3 "integrin, alpha 9" 831 rs267561 ITGA9 3680 3 37549955 NM_002207 NP_002198 C/T G507E minus 23257496 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.44 0.47 0.03 140 2 0.29 0.21 71 2 123 "by doubleHit,submitter,freq,cluster" Tolerant 0.35 2.82 16 moderately conservative 603963 3p21.3 "integrin, alpha 9" 832 rs268671 PRX 57716 19 45593454 NM_181882 NP_870998 C/T V882A minus 599856 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.29 0.32 0.15 194 3 0.24 0.08 46 2 121 "by doubleHit,freq,cluster" Tolerant 0.75 2.82 11 moderately conservative 605725 19q13.13-q13.2 periaxin 833 rs268671 PRX 57716 19 45593454 NM_181882 NP_870998 C/T V882A minus 599856 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 88 0.19 0.32 0.15 194 3 0.24 0.08 46 2 121 "by doubleHit,freq,cluster" Tolerant 0.75 2.82 11 moderately conservative 605725 19q13.13-q13.2 periaxin 834 rs268671 PRX 57716 19 45593454 NM_181882 NP_870998 C/T V882A minus 599856 1303 SEQUENOM CEPH CEPH (92) 92 0.45 0.32 0.15 194 3 0.24 0.08 46 2 121 "by doubleHit,freq,cluster" Tolerant 0.75 2.82 11 moderately conservative 605725 19q13.13-q13.2 periaxin 835 rs268673 PRX 57716 19 45593336 NM_181882 NP_870998 A/G I921M minus 508093 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.4 0.32 0.13 212 2 121 "HapMap,submitter,freq,cluster" Borderline 0.16 2.87 10 conservative 605725 19q13.13-q13.2 periaxin 836 rs268673 PRX 57716 19 45593336 NM_181882 NP_870998 A/G I921M minus 508093 1303 SEQUENOM CEPH CEPH (92) 92 0.22 0.32 0.13 212 2 121 "HapMap,submitter,freq,cluster" Borderline 0.16 2.87 10 conservative 605725 19q13.13-q13.2 periaxin 837 rs268674 PRX 57716 19 45592705 NM_181882 NP_870998 A/G G1132R minus 528679 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.05 0.07 0.05 168 2 0.02 0.01 1550 2 123 "HapMap,freq,cluster" moderately radical 605725 19q13.13-q13.2 periaxin 838 rs268674 PRX 57716 19 45592705 NM_181882 NP_870998 A/G G1132R minus 24595982 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.07 0.05 168 2 0.02 0.01 1550 2 123 "HapMap,freq,cluster" moderately radical 605725 19q13.13-q13.2 periaxin 839 rs269868 DUOX2 50506 15 43179367 NM_014080 NP_054799 C/T S1067L minus 2032138 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.02 0.03 0.03 168 2 0.2 0.23 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.464 14 Potentially intolerant 0.1 2.86 42 moderately radical 606759 15q15.3 dual oxidase 2 840 rs269868 DUOX2 50506 15 43179367 NM_014080 NP_054799 C/T S1067L minus 23462795 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.03 0.03 168 2 0.2 0.23 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.464 14 Potentially intolerant 0.1 2.86 42 moderately radical 606759 15q15.3 dual oxidase 2 841 rs283526 ATF5 22809 19 55127674 NM_012068 NP_036200 C/T P121L plus 2039819 1303 SEQUENOM CEPH CEPH (92) 92 0.02 0.02 0 92 1 120 "by doubleHit,freq,cluster" Tolerant 0.88 2.81 23 moderately conservative 606398 19q13.3 activating transcription factor 5 842 rs285584 PDZRN4 29951 12 40232806 NM_013377 NP_037509 A/G G171S plus 627828 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.13 0.14 0.01 166 2 0.2 0.21 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Possibly damaging 1.722 13 Potentially intolerant 0.1 3.06 372 moderately conservative 12q12 PDZ domain containing RING finger 4 843 rs285584 PDZRN4 29951 12 40232806 NM_013377 NP_037509 A/G G171S plus 23342080 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.14 0.01 166 2 0.2 0.21 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Possibly damaging 1.722 13 Potentially intolerant 0.1 3.06 372 moderately conservative 12q12 PDZ domain containing RING finger 4 844 rs288334 DNAJC10 54431 2 183448053 NM_018981 NP_061854 A/C H646Q minus 24151124 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.26 0.26 0 46 1 0.34 0.2 94 2 123 "by doubleHit,submitter,freq,cluster" Benign 0.187 11 Tolerant 0.67 2.9 27 conservative 607987 2q32.1 "DnaJ (Hsp40) homolog, subfamily C, member 10" 845 rs291102 PIGR 5284 1 203494873 NM_002644 NP_002635 C/T A580V minus 1342427 1303 SEQUENOM CEPH CEPH (92) 92 0.07 0.07 0 92 1 0.16 0 1494 1 100 "by doubleHit,submitter,freq,cluster" Benign 0.095 9 moderately conservative 173880 1q31-q41 polymeric immunoglobulin receptor 846 rs305974 CYP2F1 1572 19 46319708 NM_000774 NP_000765 A/G D218N plus 1609735 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.33 0.39 0.1 210 2 113 "HapMap,freq" Borderline 1.027 90 Tolerant 1 2.78 165 conservative 124070 19q13.2 "cytochrome P450, family 2, subfamily F, polypeptide 1" 847 rs305974 CYP2F1 1572 19 46319708 NM_000774 NP_000765 A/G D218N plus 1609735 1303 SEQUENOM CEPH CEPH (92) 92 0.47 0.39 0.1 210 2 113 "HapMap,freq" Borderline 1.027 90 Tolerant 1 2.78 165 conservative 124070 19q13.2 "cytochrome P450, family 2, subfamily F, polypeptide 1" 848 rs306547 DDX31 64794 9 132499968 NM_022779 NP_073616 C/T I799V plus 504735 1303 SEQUENOM CEPH CEPH (92) 92 0.41 0.41 0 92 1 121 "by cluster,freq" conservative 9q34.3 DEAD (Asp-Glu-Ala-Asp) box polypeptide 31 849 rs307821 FLT4 2324 5 179962919 NM_182925 NP_891555 G/T R1324L minus 1765465 1303 SEQUENOM CEPH CEPH (92) 92 0.12 0.12 0 92 1 100 by freq Tolerant 0.4 3.02 20 moderately radical 136352 5q34-q35 fms-related tyrosine kinase 4 850 rs309559 CSPG2 1462 5 82869125 NM_004385 NP_004376 C/T K1516R minus 731523 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.43 0.47 0.02 242 4 0.45 0.05 872 5 123 "by doubleHit,submitter,freq,cluster" Benign 0.118 5 Borderline 0.11 3.14 7 conservative 118661 5q14.3 chondroitin sulfate proteoglycan 2 (versican) 851 rs309559 CSPG2 1462 5 82869125 NM_004385 NP_004376 C/T K1516R minus 731523 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 92 0.48 0.47 0.02 242 4 0.45 0.05 872 5 123 "by doubleHit,submitter,freq,cluster" Benign 0.118 5 Borderline 0.11 3.14 7 conservative 118661 5q14.3 chondroitin sulfate proteoglycan 2 (versican) 852 rs309559 CSPG2 1462 5 82869125 NM_004385 NP_004376 C/T K1516R minus 2225096 1303 SEQUENOM CEPH CEPH (92) 92 0.48 0.47 0.02 242 4 0.45 0.05 872 5 123 "by doubleHit,submitter,freq,cluster" Benign 0.118 5 Borderline 0.11 3.14 7 conservative 118661 5q14.3 chondroitin sulfate proteoglycan 2 (versican) 853 rs309559 CSPG2 1462 5 82869125 NM_004385 NP_004376 C/T K1516R minus 24621156 1371 PERLEGEN AFD_EUR_PANEL European American (24) 44 0.45 0.47 0.02 242 4 0.45 0.05 872 5 123 "by doubleHit,submitter,freq,cluster" Benign 0.118 5 Borderline 0.11 3.14 7 conservative 118661 5q14.3 chondroitin sulfate proteoglycan 2 (versican) 854 rs310632 PRIC285 85441 20 61667251 NM_033405 NP_208384 A/G H554R minus 8378779 1303 SEQUENOM CEPH CEPH (92) 92 0.18 0.18 0 92 1 121 "by cluster,freq" conservative 20q13.33 peroxisomal proliferator-activated receptor A interacting complex 285 855 rs310791 E2F7 144455 12 75952258 NM_203394 NP_976328 A/G F72L plus 492242 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.07 0.08 0.02 168 2 0.18 0.23 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 12q21.1 E2F transcription factor 7 856 rs310791 E2F7 144455 12 75952258 NM_203394 NP_976328 A/G F72L plus 23379876 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.08 0.02 168 2 0.18 0.23 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 12q21.1 E2F transcription factor 7 857 rs310831 E2F7 144455 12 75921809 NM_203394 NP_976328 A/T H854Q plus 502756 902 AFFY Caucasian 20 0.15 0.14 0.03 80 3 0.02 0 46 1 123 "by doubleHit,submitter,freq" conservative 12q21.1 E2F transcription factor 7 858 rs310831 E2F7 144455 12 75921809 NM_203394 NP_976328 A/T H854Q plus 502756 904 AFFY CEPH 12 0.08 0.14 0.03 80 3 0.02 0 46 1 123 "by doubleHit,submitter,freq" conservative 12q21.1 E2F transcription factor 7 859 rs310831 E2F7 144455 12 75921809 NM_203394 NP_976328 A/T H854Q plus 24403096 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.14 0.03 80 3 0.02 0 46 1 123 "by doubleHit,submitter,freq" conservative 12q21.1 E2F transcription factor 7 860 rs311685 DDX43 55510 6 74182609 NM_018665 NP_061135 C/T Q629R minus 5253350 1303 SEQUENOM CEPH CEPH (92) 92 0.3 0.36 0.08 167 4 0.34 0.03 166 5 123 "by doubleHit,freq,cluster" conservative 606286 6q12-q13 DEAD (Asp-Glu-Ala-Asp) box polypeptide 43 861 rs311685 DDX43 55510 6 74182609 NM_018665 NP_061135 C/T Q629R minus 16335927 902 AFFY Caucasian 22 0.41 0.36 0.08 167 4 0.34 0.03 166 5 123 "by doubleHit,freq,cluster" conservative 606286 6q12-q13 DEAD (Asp-Glu-Ala-Asp) box polypeptide 43 862 rs311685 DDX43 55510 6 74182609 NM_018665 NP_061135 C/T Q629R minus 16335927 904 AFFY CEPH 5 0.5 0.36 0.08 167 4 0.34 0.03 166 5 123 "by doubleHit,freq,cluster" conservative 606286 6q12-q13 DEAD (Asp-Glu-Ala-Asp) box polypeptide 43 863 rs311685 DDX43 55510 6 74182609 NM_018665 NP_061135 C/T Q629R minus 24402124 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.44 0.36 0.08 167 4 0.34 0.03 166 5 123 "by doubleHit,freq,cluster" conservative 606286 6q12-q13 DEAD (Asp-Glu-Ala-Asp) box polypeptide 43 864 rs311686 DDX43 55510 6 74182596 NM_018665 NP_061135 C/T K625E minus 5384030 1303 SEQUENOM CEPH CEPH (92) 92 0.46 0.45 0.01 140 2 0.36 0.04 94 2 123 "by doubleHit,freq,cluster" moderately conservative 606286 6q12-q13 DEAD (Asp-Glu-Ala-Asp) box polypeptide 43 865 rs311686 DDX43 55510 6 74182596 NM_018665 NP_061135 C/T K625E minus 24402117 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.44 0.45 0.01 140 2 0.36 0.04 94 2 123 "by doubleHit,freq,cluster" moderately conservative 606286 6q12-q13 DEAD (Asp-Glu-Ala-Asp) box polypeptide 43 866 rs315675 ZCCHC4 29063 4 25040170 XM_376310 XP_376310 A/T L395H minus 899412 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.21 0.14 0.04 318 4 0.15 0.03 742 2 121 "HapMap,submitter,freq,cluster" Possibly damaging 1.695 8 moderately conservative 4p15.31 "zinc finger, CCHC domain containing 4" 867 rs315675 ZCCHC4 29063 4 25040170 XM_376310 XP_376310 A/T L395H minus 899412 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 92 0.09 0.14 0.04 318 4 0.15 0.03 742 2 121 "HapMap,submitter,freq,cluster" Possibly damaging 1.695 8 moderately conservative 4p15.31 "zinc finger, CCHC domain containing 4" 868 rs315675 ZCCHC4 29063 4 25040170 XM_376310 XP_376310 A/T L395H minus 2754883 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.15 0.14 0.04 318 4 0.15 0.03 742 2 121 "HapMap,submitter,freq,cluster" Possibly damaging 1.695 8 moderately conservative 4p15.31 "zinc finger, CCHC domain containing 4" 869 rs315675 ZCCHC4 29063 4 25040170 XM_376310 XP_376310 A/T L395H minus 2754883 1303 SEQUENOM CEPH CEPH (92) 92 0.18 0.14 0.04 318 4 0.15 0.03 742 2 121 "HapMap,submitter,freq,cluster" Possibly damaging 1.695 8 moderately conservative 4p15.31 "zinc finger, CCHC domain containing 4" 870 rs321937 ZNF610 162963 19 57561090 NM_173530 NP_775801 C/G R216P minus 4058648 902 AFFY Caucasian 20 0.1 0.13 0.05 32 2 0.27 0.05 66 3 121 "by doubleHit,submitter,freq,cluster" Possibly damaging 1.692 7 moderately radical 19q13.41 zinc finger protein 610 871 rs321937 ZNF610 162963 19 57561090 NM_173530 NP_775801 C/G R216P minus 4058648 904 AFFY CEPH 12 0.17 0.13 0.05 32 2 0.27 0.05 66 3 121 "by doubleHit,submitter,freq,cluster" Possibly damaging 1.692 7 moderately radical 19q13.41 zinc finger protein 610 872 rs324420 FAAH 2166 1 46582781 NM_001441 NP_001432 A/C P129T plus 587534 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 12 0.42 0.24 0.05 224 3 0.19 0.18 32 2 121 "HapMap,doubleHit,submitter,freq,cluster" Possibly damaging 1.945 9 Borderline 0.13 2.79 18 conservative 602935 1p35-p34 fatty acid amide hydrolase 873 rs324420 FAAH 2166 1 46582781 NM_001441 NP_001432 A/C P129T plus 587534 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.23 0.24 0.05 224 3 0.19 0.18 32 2 121 "HapMap,doubleHit,submitter,freq,cluster" Possibly damaging 1.945 9 Borderline 0.13 2.79 18 conservative 602935 1p35-p34 fatty acid amide hydrolase 874 rs324420 FAAH 2166 1 46582781 NM_001441 NP_001432 A/C P129T plus 587534 1303 SEQUENOM CEPH CEPH (92) 92 0.23 0.24 0.05 224 3 0.19 0.18 32 2 121 "HapMap,doubleHit,submitter,freq,cluster" Possibly damaging 1.945 9 Borderline 0.13 2.79 18 conservative 602935 1p35-p34 fatty acid amide hydrolase 875 rs344140 ShrmL 57619 4 78017341 NM_020859 NP_065910 C/G G278A plus 569841 1303 SEQUENOM CEPH CEPH (92) 92 0.17 0.17 0 92 1 120 "by doubleHit,freq,cluster" moderately conservative 604570 4q21.22 Shroom-related protein 876 rs344141 ShrmL 57619 4 78017910 NM_020859 NP_065910 C/G P468A plus 1335241 1303 SEQUENOM CEPH CEPH (92) 92 0.39 0.39 0 92 1 120 "by doubleHit,freq,cluster" conservative 604570 4q21.22 Shroom-related protein 877 rs346821 FLJ10060 55065 17 4877696 NM_017986 NP_060456 A/G A271V plus 609695 1303 SEQUENOM CEPH CEPH (92) 92 0.28 0.28 0 92 1 0.22 0 1498 1 121 "by doubleHit,freq,cluster" Benign 0.228 11 moderately conservative 607883 17p13.3 putative G-protein coupled receptor GPCR42 878 rs346822 FLJ10060 55065 17 4878299 NM_017986 NP_060456 A/G Q70R minus 1322665 1303 SEQUENOM CEPH CEPH (92) 92 0.09 0.07 0.03 140 2 0.1 0.08 94 2 123 "by doubleHit,freq,cluster" Benign 0.394 11 conservative 607883 17p13.3 putative G-protein coupled receptor GPCR42 879 rs346822 FLJ10060 55065 17 4878299 NM_017986 NP_060456 A/G Q70R minus 24213524 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.07 0.03 140 2 0.1 0.08 94 2 123 "by doubleHit,freq,cluster" Benign 0.394 11 conservative 607883 17p13.3 putative G-protein coupled receptor GPCR42 880 rs351111 PRTN3 5657 19 795020 NM_002777 NP_002768 A/G V119I plus 1745256 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.43 0.43 0.01 212 2 102 "HapMap,submitter,freq" Benign 0.469 20 conservative 177020 19p13.3 "proteinase 3 (serine proteinase, neutrophil, Wegener granulomatosis autoantigen)" 881 rs351111 PRTN3 5657 19 795020 NM_002777 NP_002768 A/G V119I plus 1745256 1303 SEQUENOM CEPH CEPH (92) 92 0.44 0.43 0.01 212 2 102 "HapMap,submitter,freq" Benign 0.469 20 conservative 177020 19p13.3 "proteinase 3 (serine proteinase, neutrophil, Wegener granulomatosis autoantigen)" 882 rs352493 SIRT6 51548 19 4131836 NM_016539 NP_057623 C/T S46N plus 566893 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 94 0.05 0.04 0.03 232 3 0.19 0.13 134 4 123 "by cluster,freq" Benign 0.23 9 Tolerant 0.22 2.75 25 conservative 606211 19p13.3 sirtuin (silent mating type information regulation 2 homolog) 6 (S. cerevisiae) 883 rs352493 SIRT6 51548 19 4131836 NM_016539 NP_057623 C/T S46N plus 566893 1303 SEQUENOM CEPH CEPH (92) 92 0.01 0.04 0.03 232 3 0.19 0.13 134 4 123 "by cluster,freq" Benign 0.23 9 Tolerant 0.22 2.75 25 conservative 606211 19p13.3 sirtuin (silent mating type information regulation 2 homolog) 6 (S. cerevisiae) 884 rs352493 SIRT6 51548 19 4131836 NM_016539 NP_057623 C/T S46N plus 24081883 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.07 0.04 0.03 232 3 0.19 0.13 134 4 123 "by cluster,freq" Benign 0.23 9 Tolerant 0.22 2.75 25 conservative 606211 19p13.3 sirtuin (silent mating type information regulation 2 homolog) 6 (S. cerevisiae) 885 rs357564 PTCH 5727 9 95289149 NM_000264 NP_000255 A/G P1315L plus 3176045 619 WICVAR MITOGPOP6 CORIELL Mixed 28 0.32 0.4 0.04 212 2 123 by freq moderately conservative 601309 9q22.3 patched homolog (Drosophila) 886 rs357564 PTCH 5727 9 95289149 NM_000264 NP_000255 A/G P1315L plus 24796376 1303 SEQUENOM CEPH CEPH (92) 184 0.41 0.4 0.04 212 2 123 by freq moderately conservative 601309 9q22.3 patched homolog (Drosophila) 887 rs359974 IHH 3549 2 219755696 XM_050846 XP_050846 C/T M1I plus 548265 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.2 0.23 0.04 212 2 121 "HapMap,doubleHit,submitter,freq,cluster" conservative 600726 2q33-q35 Indian hedgehog homolog (Drosophila) 888 rs359974 IHH 3549 2 219755696 XM_050846 XP_050846 C/T M1I plus 17685878 1303 SEQUENOM CEPH CEPH (92) 92 0.26 0.23 0.04 212 2 121 "HapMap,doubleHit,submitter,freq,cluster" conservative 600726 2q33-q35 Indian hedgehog homolog (Drosophila) 889 rs360057 LEFTB 10637 1 222381298 NM_020997 NP_066277 G/T D322A plus 3063905 1303 SEQUENOM CEPH CEPH (92) 92 0.25 0.25 0 92 1 119 "by doubleHit,freq" Potentially damaging 1.268 7 Tolerant 0.77 2.85 17 moderately radical 603037 1q42.1 "left-right determination, factor B" 890 rs363294 PDZK8 118987 10 119033544 NM_173791 NP_776152 C/T R897Q plus 1467278 1303 SEQUENOM CEPH CEPH (92) 92 0.16 0.14 0.04 140 2 0.02 0 46 1 123 "by submitter,freq,cluster" conservative 10q26.12 PDZ domain containing 8 891 rs363294 PDZK8 118987 10 119033544 NM_173791 NP_776152 C/T R897Q plus 24568899 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.14 0.04 140 2 0.02 0 46 1 123 "by submitter,freq,cluster" conservative 10q26.12 PDZ domain containing 8 892 rs363504 GRIK1 2897 21 29847799 NM_000830 NP_000821 C/T L902S minus 4010646 634 PERLEGEN NCBI|NIHPDR NIHPDR 11 0.18 0.18 0 11 1 102 "by submitter,freq,cluster" moderately radical 138245 21q22.11 "glutamate receptor, ionotropic, kainate 1" 893 rs366439 EBAF 7044 1 222434413 NM_003240 NP_003231 A/G S92L plus 464983 1303 SEQUENOM CEPH CEPH (92) 46 0.5 0.5 0 46 1 0.25 0 1464 1 98 "by cluster,freq" moderately radical 601877 1q42.1 "endometrial bleeding associated factor (left-right determination, factor A; transforming growth factor beta superfamily)" 894 rs370429 PCM1 5108 8 17893427 NM_006197 NP_006188 A/G T1543I minus 4092407 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.03 0.03 0.01 260 3 0.24 0.05 92 2 123 "HapMap,submitter,freq,cluster" moderately conservative 600299 8p22-p21.3 pericentriolar material 1 895 rs370429 PCM1 5108 8 17893427 NM_006197 NP_006188 A/G T1543I minus 4092407 1303 SEQUENOM CEPH CEPH (92) 92 0.04 0.03 0.01 260 3 0.24 0.05 92 2 123 "HapMap,submitter,freq,cluster" moderately conservative 600299 8p22-p21.3 pericentriolar material 1 896 rs370429 PCM1 5108 8 17893427 NM_006197 NP_006188 A/G T1543I minus 23980890 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.03 0.01 260 3 0.24 0.05 92 2 123 "HapMap,submitter,freq,cluster" moderately conservative 600299 8p22-p21.3 pericentriolar material 1 897 rs373496 TNFRSF17 608 16 11967664 NM_001192 NP_001183 C/T N81S minus 16341954 693 EGP_SNPS PDR90 NIHPDR 174 0.03 0.03 0.01 266 2 121 "by cluster,freq" conservative 109545 16p13.1 "tumor necrosis factor receptor superfamily, member 17" 898 rs373496 TNFRSF17 608 16 11967664 NM_001192 NP_001183 C/T N81S minus 16728545 1303 SEQUENOM CEPH CEPH (92) 92 0.02 0.03 0.01 266 2 121 "by cluster,freq" conservative 109545 16p13.1 "tumor necrosis factor receptor superfamily, member 17" 899 rs373572 RAD18 56852 3 8930389 NM_020165 NP_064550 A/G R302Q minus 2293973 885 TSC-CSHL HapMap-CEPH-30-trios 100 0.18 0.18 0 240 3 0.33 0.01 92 2 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.9 5 conservative 605256 3p25-p24 RAD18 homolog (S. cerevisiae) 900 rs373572 RAD18 56852 3 8930389 NM_020165 NP_064550 A/G R302Q minus 2293973 1303 SEQUENOM CEPH CEPH (92) 92 0.18 0.18 0 240 3 0.33 0.01 92 2 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.9 5 conservative 605256 3p25-p24 RAD18 homolog (S. cerevisiae) 901 rs373572 RAD18 56852 3 8930389 NM_020165 NP_064550 A/G R302Q minus 23886577 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.19 0.18 0 240 3 0.33 0.01 92 2 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.9 5 conservative 605256 3p25-p24 RAD18 homolog (S. cerevisiae) 902 rs382627 FCGR2A 2212 1 158300860 NM_021642 NP_067674 C/T L272P plus 16450684 1303 SEQUENOM CEPH CEPH (92) 92 0.46 0.46 0 92 1 0.02 0 46 1 123 "by doubleHit,cluster" moderately conservative 146790 1q23 "Fc fragment of IgG, low affinity IIa, receptor for (CD32)" 903 rs383369 LILRB2 10288 19 59475942 NM_005874 NP_005865 C/T H20R plus 5464668 1303 SEQUENOM CEPH CEPH (92) 92 0.24 0.24 0 92 1 108 "by doubleHit,freq" Benign 0.659 61 Tolerant 0.47 2.97 51 conservative 604815 19q13.4 "leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 2" 904 rs386056 LILRB2 10288 19 59474731 NM_005874 NP_005865 A/G V235M minus 497545 1303 SEQUENOM CEPH CEPH (92) 92 0.21 0.21 0 92 1 120 "by cluster,freq" Benign 0.277 63 Intolerant 0.02 2.78 214 conservative 604815 19q13.4 "leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 2" 905 rs388685 ZNF45 7596 19 49110520 NM_003425 NP_003416 C/G P303R plus 24685147 1371 PERLEGEN AFD_EUR_PANEL European American (24) 24 0.5 0.48 0.01 208 2 0.26 0.05 1493 3 123 "by doubleHit,submitter,freq,cluster" Benign 0.927 13 Intolerant 0.03 2.73 29 moderately radical 601781 19q13.2 zinc finger protein 45 (a Kruppel-associated box (KRAB) domain polypeptide) 906 rs388685 ZNF45 7596 19 49110520 NM_003425 NP_003416 C/G P303R plus 24811382 1303 SEQUENOM CEPH CEPH (92) 184 0.48 0.48 0.01 208 2 0.26 0.05 1493 3 123 "by doubleHit,submitter,freq,cluster" Benign 0.927 13 Intolerant 0.03 2.73 29 moderately radical 601781 19q13.2 zinc finger protein 45 (a Kruppel-associated box (KRAB) domain polypeptide) 907 rs388706 ZNF45 7596 19 49110533 NM_003425 NP_003416 C/T T299A plus 2995829 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 78 0.47 0.43 0.06 218 3 0.19 0.09 242 4 123 "by doubleHit,freq,cluster" Benign 0.891 13 Potentially intolerant 0.1 2.73 29 moderately conservative 601781 19q13.2 zinc finger protein 45 (a Kruppel-associated box (KRAB) domain polypeptide) 908 rs388706 ZNF45 7596 19 49110533 NM_003425 NP_003416 C/T T299A plus 2995829 1303 SEQUENOM CEPH CEPH (92) 92 0.38 0.43 0.06 218 3 0.19 0.09 242 4 123 "by doubleHit,freq,cluster" Benign 0.891 13 Potentially intolerant 0.1 2.73 29 moderately conservative 601781 19q13.2 zinc finger protein 45 (a Kruppel-associated box (KRAB) domain polypeptide) 909 rs388706 ZNF45 7596 19 49110533 NM_003425 NP_003416 C/T T299A plus 24685149 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.48 0.43 0.06 218 3 0.19 0.09 242 4 123 "by doubleHit,freq,cluster" Benign 0.891 13 Potentially intolerant 0.1 2.73 29 moderately conservative 601781 19q13.2 zinc finger protein 45 (a Kruppel-associated box (KRAB) domain polypeptide) 910 rs390659 RDS 5961 6 42774142 NM_000322 NP_000313 C/G Q304E plus 505147 1303 SEQUENOM CEPH CEPH (92) 92 0.06 0.06 0 92 1 121 "by cluster,freq" Possibly damaging 1.528 27 conservative 179605 6p21.2-p12.3 "retinal degeneration, slow" 911 rs394558 TATDN2 9797 3 10277172 XM_376203 XP_376203 A/G V256I plus 4078742 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.42 0.36 0.09 260 3 0.16 0.18 88 2 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 3p25.3 TatD DNase domain containing 1 912 rs394558 TATDN2 9797 3 10277172 XM_376203 XP_376203 A/G V256I plus 4078742 1303 SEQUENOM CEPH CEPH (92) 92 0.34 0.36 0.09 260 3 0.16 0.18 88 2 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 3p25.3 TatD DNase domain containing 1 913 rs394558 TATDN2 9797 3 10277172 XM_376203 XP_376203 A/G V256I plus 23241729 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.23 0.36 0.09 260 3 0.16 0.18 88 2 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 3p25.3 TatD DNase domain containing 1 914 rs394732 BCAS1 8537 20 52108595 NM_003657 NP_003648 G/T Q24K plus 2993255 760 TSC-CSHL CEL_CAUCASIAN CELERA Caucasians (30) 60 0.4 0.43 0.01 546 4 0.29 0.02 208 4 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 602968 20q13.2-q13.3 breast carcinoma amplified sequence 1 915 rs394732 BCAS1 8537 20 52108595 NM_003657 NP_003648 G/T Q24K plus 2993255 761 TSC-CSHL CEL_CAUCASIAN_CEPH CELERA CEPH Caucasians (661) 320 0.43 0.43 0.01 546 4 0.29 0.02 208 4 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 602968 20q13.2-q13.3 breast carcinoma amplified sequence 1 916 rs394732 BCAS1 8537 20 52108595 NM_003657 NP_003648 G/T Q24K plus 2993255 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.42 0.43 0.01 546 4 0.29 0.02 208 4 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 602968 20q13.2-q13.3 breast carcinoma amplified sequence 1 917 rs394732 BCAS1 8537 20 52108595 NM_003657 NP_003648 G/T Q24K plus 24558206 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.44 0.43 0.01 546 4 0.29 0.02 208 4 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 602968 20q13.2-q13.3 breast carcinoma amplified sequence 1 918 rs396716 FCGR3A 2214 1 158327651 NM_000569 NP_000560 C/T Y194H minus 515045 885 TSC-CSHL HapMap-CEPH-30-trios 114 0.01 0.17 0.25 206 2 120 "HapMap,doubleHit,cluster" Benign 0.383 23 Tolerant 0.55 2.82 48 moderately conservative 146740 1q23 "Fc fragment of IgG, low affinity IIIa, receptor for (CD16)" 919 rs396716 FCGR3A 2214 1 158327651 NM_000569 NP_000560 C/T Y194H minus 515045 1303 SEQUENOM CEPH CEPH (92) 92 0.36 0.17 0.25 206 2 120 "HapMap,doubleHit,cluster" Benign 0.383 23 Tolerant 0.55 2.82 48 moderately conservative 146740 1q23 "Fc fragment of IgG, low affinity IIIa, receptor for (CD16)" 920 rs396991 FCGR3A 2214 1 158327597 NM_000569 NP_000560 G/T F212V minus 515482 1303 SEQUENOM CEPH CEPH (92) 92 0.45 0.45 0 92 1 121 "by doubleHit,cluster" Benign 0.202 23 Tolerant 0.33 2.84 40 conservative 146740 1q23 "Fc fragment of IgG, low affinity IIIa, receptor for (CD16)" 921 rs398829 ADAMTS2 9509 5 178567278 NM_014244 NP_055059 A/G V245I minus 17097424 1303 SEQUENOM CEPH CEPH (92) 92 0.25 0.25 0 92 1 0.36 0 1490 1 121 "by doubleHit,freq,cluster" Benign 0.883 12 Tolerant 0.85 2.78 21 conservative 604539 5qter "a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 2" 922 rs399098 ZNF45 7596 19 49110664 NM_003425 NP_003416 A/G R255K minus 2995828 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.39 0.41 0.04 256 3 0.39 0.09 774 3 123 "HapMap,doubleHit,freq,cluster" Benign 0.067 13 Tolerant 1 2.73 29 conservative 601781 19q13.2 zinc finger protein 45 (a Kruppel-associated box (KRAB) domain polypeptide) 923 rs399098 ZNF45 7596 19 49110664 NM_003425 NP_003416 A/G R255K minus 2995828 1303 SEQUENOM CEPH CEPH (92) 92 0.4 0.41 0.04 256 3 0.39 0.09 774 3 123 "HapMap,doubleHit,freq,cluster" Benign 0.067 13 Tolerant 1 2.73 29 conservative 601781 19q13.2 zinc finger protein 45 (a Kruppel-associated box (KRAB) domain polypeptide) 924 rs399098 ZNF45 7596 19 49110664 NM_003425 NP_003416 A/G R255K minus 24197170 1371 PERLEGEN AFD_EUR_PANEL European American (24) 44 0.48 0.41 0.04 256 3 0.39 0.09 774 3 123 "HapMap,doubleHit,freq,cluster" Benign 0.067 13 Tolerant 1 2.73 29 conservative 601781 19q13.2 zinc finger protein 45 (a Kruppel-associated box (KRAB) domain polypeptide) 925 rs402680 AOC3 8639 17 38257119 NM_003734 NP_003725 C/T R78Q minus 24811429 1303 SEQUENOM CEPH CEPH (92) 184 0.3 0.3 0 184 1 123 "by cluster,freq" Benign 0.071 15 Tolerant 0.24 2.85 24 conservative 603735 17q21 "amine oxidase, copper containing 3 (vascular adhesion protein 1)" 926 rs403016 FCGR3A 2214 1 158331477 NM_000569 NP_000560 C/G R72S plus 24788817 1303 SEQUENOM CEPH CEPH (92) 184 0.45 0.4 0.07 368 2 123 "by doubleHit,submitter,freq,cluster" Benign 0.785 23 Tolerant 0.45 2.82 48 moderately radical 146740 1q23 "Fc fragment of IgG, low affinity IIIa, receptor for (CD16)" 927 rs403016 FCGR3A 2214 1 158331477 NM_000569 NP_000560 C/G R72S plus 24796109 1303 SEQUENOM CEPH CEPH (92) 184 0.35 0.4 0.07 368 2 123 "by doubleHit,submitter,freq,cluster" Benign 0.785 23 Tolerant 0.45 2.82 48 moderately radical 146740 1q23 "Fc fragment of IgG, low affinity IIIa, receptor for (CD16)" 928 rs407731 ZNF45 7596 19 49109917 NM_003425 NP_003416 A/G R504K minus 1315616 1303 SEQUENOM CEPH CEPH (92) 92 0.27 0.34 0.14 140 2 0.21 0.01 94 2 123 "by doubleHit,submitter,freq,cluster" Benign 0.225 11 Tolerant 0.33 2.74 28 conservative 601781 19q13.2 zinc finger protein 45 (a Kruppel-associated box (KRAB) domain polypeptide) 929 rs407731 ZNF45 7596 19 49109917 NM_003425 NP_003416 A/G R504K minus 24685139 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.48 0.34 0.14 140 2 0.21 0.01 94 2 123 "by doubleHit,submitter,freq,cluster" Benign 0.225 11 Tolerant 0.33 2.74 28 conservative 601781 19q13.2 zinc finger protein 45 (a Kruppel-associated box (KRAB) domain polypeptide) 930 rs408038 AOC3 8639 17 38257397 NM_003734 NP_003725 C/T V171M minus 24796534 1303 SEQUENOM CEPH CEPH (92) 184 0.27 0.18 0.13 368 2 123 by freq Benign 0.246 15 Borderline 0.16 2.85 24 conservative 603735 17q21 "amine oxidase, copper containing 3 (vascular adhesion protein 1)" 931 rs408038 AOC3 8639 17 38257397 NM_003734 NP_003725 C/T V171M minus 24811443 1303 SEQUENOM CEPH CEPH (92) 184 0.08 0.18 0.13 368 2 123 by freq Benign 0.246 15 Borderline 0.16 2.85 24 conservative 603735 17q21 "amine oxidase, copper containing 3 (vascular adhesion protein 1)" 932 rs412750 PCM1 5108 8 17840662 NM_006197 NP_006188 A/G N159S plus 541750 1303 SEQUENOM CEPH CEPH (92) 92 0.03 0.03 0 92 1 121 "by doubleHit,freq,cluster" conservative 600299 8p22-p21.3 pericentriolar material 1 933 rs414352 RP1 6101 8 55704066 NM_006269 NP_006260 C/T S1691P plus 544417 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.23 0.23 0.04 260 3 0.32 0.23 90 2 123 "HapMap,doubleHit,submitter,freq" Benign 0.284 6 moderately conservative 603937 8q11-q13 retinitis pigmentosa 1 (autosomal dominant) 934 rs414352 RP1 6101 8 55704066 NM_006269 NP_006260 C/T S1691P plus 544417 1303 SEQUENOM CEPH CEPH (92) 92 0.2 0.23 0.04 260 3 0.32 0.23 90 2 123 "HapMap,doubleHit,submitter,freq" Benign 0.284 6 moderately conservative 603937 8q11-q13 retinitis pigmentosa 1 (autosomal dominant) 935 rs414352 RP1 6101 8 55704066 NM_006269 NP_006260 C/T S1691P plus 24077580 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.29 0.23 0.04 260 3 0.32 0.23 90 2 123 "HapMap,doubleHit,submitter,freq" Benign 0.284 6 moderately conservative 603937 8q11-q13 retinitis pigmentosa 1 (autosomal dominant) 936 rs414408 COL1A2 1278 7 93686590 NM_000089 NP_000080 C/T A483V plus 544512 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 83 0.16 0.16 0 83 1 80 by freq Tolerant 0.29 3.03 75 moderately conservative 120160 7q22.1 "collagen, type I, alpha 2" 937 rs417012 PAPPA 5069 9 115996019 NM_002581 NP_002572 G/T S5I plus 548739 1303 SEQUENOM CEPH CEPH (92) 92 0.06 0.06 0 92 1 80 by freq moderately radical 176385 9q33.2 pregnancy-associated plasma protein A 938 rs428073 JIK 51347 12 117145471 NM_016281 NP_057365 C/T S47N plus 1994738 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.29 0.29 0 120 1 121 "HapMap,freq,cluster" Benign 0.503 21 conservative 12q STE20-like kinase 939 rs428785 ADAMTS1 9510 21 27138466 NM_006988 NP_008919 C/G A210P plus 568349 1303 SEQUENOM CEPH CEPH (92) 92 0.42 0.33 0.18 140 2 0.3 0.26 94 2 123 "by doubleHit,freq,cluster" conservative 605174 21q21.2 "a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 1" 940 rs428785 ADAMTS1 9510 21 27138466 NM_006988 NP_008919 C/G A210P plus 24024745 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.33 0.18 140 2 0.3 0.26 94 2 123 "by doubleHit,freq,cluster" conservative 605174 21q21.2 "a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 1" 941 rs428888 FCGR3A 2214 1 158331341 NM_000569 NP_000560 C/T D118N plus 5518768 1303 SEQUENOM CEPH CEPH (92) 92 0.38 0.38 0 92 1 116 "by doubleHit,freq,cluster" Benign 0.084 23 Tolerant 1 2.82 48 conservative 146740 1q23 "Fc fragment of IgG, low affinity IIIa, receptor for (CD16)" 942 rs429358 APOE 348 19 50103781 NM_000041 NP_000032 C/T C130R plus 870163 563 DEBNICK MDECODE-1 European-Americans 48 0.12 0.15 0.02 1953 3 0.1 0 96 2 123 "by doubleHit,freq,cluster" Benign 0.62 29 Tolerant 1 2.79 33 radical 107741 19q13.2 apolipoprotein E 943 rs429358 APOE 348 19 50103781 NM_000041 NP_000032 C/T C130R plus 870163 564 DEBNICK MDECODE-2 Finnish 48 0.23 0.15 0.02 1953 3 0.1 0 96 2 123 "by doubleHit,freq,cluster" Benign 0.62 29 Tolerant 1 2.79 33 radical 107741 19q13.2 apolipoprotein E 944 rs429358 APOE 348 19 50103781 NM_000041 NP_000032 C/T C130R plus 12568607 887 CUORCGL AMERICAN CAUCASIANS American Caucasians 1857 0.15 0.15 0.02 1953 3 0.1 0 96 2 123 "by doubleHit,freq,cluster" Benign 0.62 29 Tolerant 1 2.79 33 radical 107741 19q13.2 apolipoprotein E 945 rs430554 SNF1LK 150094 21 43661983 NM_173354 NP_775490 A/G A615V plus 571239 1303 SEQUENOM CEPH CEPH (92) 92 0.34 0.34 0 92 1 121 "by doubleHit,freq,cluster" moderately conservative 605705 21q22.3 SNF1-like kinase 946 rs430665 U2AF1L1 7310 5 112256566 NM_005083 NP_005074 C/T S444N minus 571422 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 24 0.21 0.35 0.11 244 4 0.34 0.1 132 4 123 "by cluster,freq" conservative 601079 5q22 U2(RNU2) small nuclear RNA auxillary factor 1-like 1 947 rs430665 U2AF1L1 7310 5 112256566 NM_005083 NP_005074 C/T S444N minus 571422 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 80 0.29 0.35 0.11 244 4 0.34 0.1 132 4 123 "by cluster,freq" conservative 601079 5q22 U2(RNU2) small nuclear RNA auxillary factor 1-like 1 948 rs430665 U2AF1L1 7310 5 112256566 NM_005083 NP_005074 C/T S444N minus 1998866 1303 SEQUENOM CEPH CEPH (92) 92 0.46 0.35 0.11 244 4 0.34 0.1 132 4 123 "by cluster,freq" conservative 601079 5q22 U2(RNU2) small nuclear RNA auxillary factor 1-like 1 949 rs430665 U2AF1L1 7310 5 112256566 NM_005083 NP_005074 C/T S444N minus 23418331 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.29 0.35 0.11 244 4 0.34 0.1 132 4 123 "by cluster,freq" conservative 601079 5q22 U2(RNU2) small nuclear RNA auxillary factor 1-like 1 950 rs434473 ALOX12 239 17 6845658 NM_000697 NP_000688 A/G N322S plus 577623 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.36 0.39 0.1 446 6 0.28 0.02 1172 4 120 "HapMap,freq,cluster" Benign 0.274 24 Tolerant 0.25 2.77 32 conservative 152391 17p13.1 arachidonate 12-lipoxygenase 951 rs434473 ALOX12 239 17 6845658 NM_000697 NP_000688 A/G N322S plus 577623 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 90 0.44 0.39 0.1 446 6 0.28 0.02 1172 4 120 "HapMap,freq,cluster" Benign 0.274 24 Tolerant 0.25 2.77 32 conservative 152391 17p13.1 arachidonate 12-lipoxygenase 952 rs434473 ALOX12 239 17 6845658 NM_000697 NP_000688 A/G N322S plus 3255020 506 NCBI NIHPDR NIHPDR 86 0.4 0.39 0.1 446 6 0.28 0.02 1172 4 120 "HapMap,freq,cluster" Benign 0.274 24 Tolerant 0.25 2.77 32 conservative 152391 17p13.1 arachidonate 12-lipoxygenase 953 rs434473 ALOX12 239 17 6845658 NM_000697 NP_000688 A/G N322S plus 16343724 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.37 0.39 0.1 446 6 0.28 0.02 1172 4 120 "HapMap,freq,cluster" Benign 0.274 24 Tolerant 0.25 2.77 32 conservative 152391 17p13.1 arachidonate 12-lipoxygenase 954 rs434473 ALOX12 239 17 6845658 NM_000697 NP_000688 A/G N322S plus 16343724 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.47 0.39 0.1 446 6 0.28 0.02 1172 4 120 "HapMap,freq,cluster" Benign 0.274 24 Tolerant 0.25 2.77 32 conservative 152391 17p13.1 arachidonate 12-lipoxygenase 955 rs434473 ALOX12 239 17 6845658 NM_000697 NP_000688 A/G N322S plus 16343724 1303 SEQUENOM CEPH CEPH (92) 92 0.23 0.39 0.1 446 6 0.28 0.02 1172 4 120 "HapMap,freq,cluster" Benign 0.274 24 Tolerant 0.25 2.77 32 conservative 152391 17p13.1 arachidonate 12-lipoxygenase 956 rs438287 AOC3 8639 17 38257835 NM_003734 NP_003725 A/G Y317H minus 5494071 1303 SEQUENOM CEPH CEPH (92) 92 0.28 0.28 0 92 1 123 by freq Probably damaging 2.092 15 Tolerant 0.8 2.82 27 moderately conservative 603735 17q21 "amine oxidase, copper containing 3 (vascular adhesion protein 1)" 957 rs438766 SIM1 6492 6 101003980 NM_005068 NP_005059 A/G L175F plus 3060752 1303 SEQUENOM CEPH CEPH (92) 92 0.44 0.44 0 92 1 96 by freq Potentially damaging 1.435 7 Borderline 0.18 2.76 123 conservative 603128 6q16.3-q21 single-minded homolog 1 (Drosophila) 958 rs443082 FCGR3A 2214 1 158327683 NM_000569 NP_000560 A/G G183D minus 591980 1303 SEQUENOM CEPH CEPH (92) 92 0.11 0.13 0.02 276 2 123 "by doubleHit,freq,cluster" Benign 0.409 23 Potentially intolerant 0.08 2.85 46 moderately conservative 146740 1q23 "Fc fragment of IgG, low affinity IIIa, receptor for (CD16)" 959 rs443082 FCGR3A 2214 1 158327683 NM_000569 NP_000560 A/G G183D minus 24820795 1303 SEQUENOM CEPH CEPH (92) 184 0.14 0.13 0.02 276 2 123 "by doubleHit,freq,cluster" Benign 0.409 23 Potentially intolerant 0.08 2.85 46 moderately conservative 146740 1q23 "Fc fragment of IgG, low affinity IIIa, receptor for (CD16)" 960 rs444772 RP1 6101 8 55701610 NM_006269 NP_006260 A/G R872H plus 594770 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.23 0.18 0.08 212 2 0.37 0 1486 1 123 "HapMap,submitter,freq,cluster" Benign 0.225 6 conservative 603937 8q11-q13 retinitis pigmentosa 1 (autosomal dominant) 961 rs444772 RP1 6101 8 55701610 NM_006269 NP_006260 A/G R872H plus 594770 1303 SEQUENOM CEPH CEPH (92) 92 0.12 0.18 0.08 212 2 0.37 0 1486 1 123 "HapMap,submitter,freq,cluster" Benign 0.225 6 conservative 603937 8q11-q13 retinitis pigmentosa 1 (autosomal dominant) 962 rs446227 RP1 6101 8 55704003 NM_006269 NP_006260 A/G A1670T plus 597189 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.23 0.2 0.08 260 3 0.27 0.3 92 2 123 "HapMap,submitter,freq" Benign 0.211 6 moderately conservative 603937 8q11-q13 retinitis pigmentosa 1 (autosomal dominant) 963 rs446227 RP1 6101 8 55704003 NM_006269 NP_006260 A/G A1670T plus 597189 1303 SEQUENOM CEPH CEPH (92) 92 0.12 0.2 0.08 260 3 0.27 0.3 92 2 123 "HapMap,submitter,freq" Benign 0.211 6 moderately conservative 603937 8q11-q13 retinitis pigmentosa 1 (autosomal dominant) 964 rs446227 RP1 6101 8 55704003 NM_006269 NP_006260 A/G A1670T plus 24077575 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.29 0.2 0.08 260 3 0.27 0.3 92 2 123 "HapMap,submitter,freq" Benign 0.211 6 moderately conservative 603937 8q11-q13 retinitis pigmentosa 1 (autosomal dominant) 965 rs448740 FCGR3A 2214 1 158331391 NM_000569 NP_000560 C/T S101N plus 5523031 1303 SEQUENOM CEPH CEPH (92) 92 0.31 0.31 0 92 1 108 "by doubleHit,freq,cluster" Benign 0.221 23 Tolerant 0.22 2.82 48 conservative 146740 1q23 "Fc fragment of IgG, low affinity IIIa, receptor for (CD16)" 966 rs450046 PRODH 5625 22 17275558 NM_016335 NP_057419 C/T R521Q plus 7993762 1303 SEQUENOM CEPH CEPH (92) 92 0.12 0.09 0.05 140 2 0.15 0.13 94 2 123 "by cluster,freq" Borderline 1.052 7 Tolerant 0.61 2.8 28 conservative 606810 22q11.21 proline dehydrogenase (oxidase) 1 967 rs450046 PRODH 5625 22 17275558 NM_016335 NP_057419 C/T R521Q plus 23788056 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.09 0.05 140 2 0.15 0.13 94 2 123 "by cluster,freq" Borderline 1.052 7 Tolerant 0.61 2.8 28 conservative 606810 22q11.21 proline dehydrogenase (oxidase) 1 968 rs451195 PPIC 5480 5 122387539 NM_000943 NP_000934 C/T N190S plus 605510 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 24 0.25 0.32 0.09 374 5 0.06 0.03 116 3 123 "HapMap,doubleHit,submitter,freq" Benign 0.044 71 Tolerant 0.45 2.75 291 conservative 123842 5q23.2 peptidylprolyl isomerase C (cyclophilin C) 969 rs451195 PPIC 5480 5 122387539 NM_000943 NP_000934 C/T N190S plus 605510 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 94 0.35 0.32 0.09 374 5 0.06 0.03 116 3 123 "HapMap,doubleHit,submitter,freq" Benign 0.044 71 Tolerant 0.45 2.75 291 conservative 123842 5q23.2 peptidylprolyl isomerase C (cyclophilin C) 970 rs451195 PPIC 5480 5 122387539 NM_000943 NP_000934 C/T N190S plus 605510 885 TSC-CSHL HapMap-CEPH-30-trios 116 0.4 0.32 0.09 374 5 0.06 0.03 116 3 123 "HapMap,doubleHit,submitter,freq" Benign 0.044 71 Tolerant 0.45 2.75 291 conservative 123842 5q23.2 peptidylprolyl isomerase C (cyclophilin C) 971 rs451195 PPIC 5480 5 122387539 NM_000943 NP_000934 C/T N190S plus 605510 1303 SEQUENOM CEPH CEPH (92) 92 0.19 0.32 0.09 374 5 0.06 0.03 116 3 123 "HapMap,doubleHit,submitter,freq" Benign 0.044 71 Tolerant 0.45 2.75 291 conservative 123842 5q23.2 peptidylprolyl isomerase C (cyclophilin C) 972 rs451195 PPIC 5480 5 122387539 NM_000943 NP_000934 C/T N190S plus 24346271 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.35 0.32 0.09 374 5 0.06 0.03 116 3 123 "HapMap,doubleHit,submitter,freq" Benign 0.044 71 Tolerant 0.45 2.75 291 conservative 123842 5q23.2 peptidylprolyl isomerase C (cyclophilin C) 973 rs457947 ADAMTS5 11096 21 27260169 NM_007038 NP_008969 C/G G138A plus 2857357 1303 SEQUENOM CEPH CEPH (92) 92 0.11 0.11 0 92 1 100 by freq moderately conservative 605007 21q21.3 "a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2)" 974 rs458017 REV3L 5980 6 111802784 NM_002912 NP_002903 C/T Y1078C plus 617419 1303 SEQUENOM CEPH CEPH (92) 92 0.07 0.08 0.01 278 3 0.11 0 46 1 123 "by cluster,freq" radical 602776 6q21 "REV3-like, catalytic subunit of DNA polymerase zeta (yeast)" 975 rs458017 REV3L 5980 6 111802784 NM_002912 NP_002903 C/T Y1078C plus 4479764 506 NCBI NIHPDR NIHPDR 138 0.08 0.08 0.01 278 3 0.11 0 46 1 123 "by cluster,freq" radical 602776 6q21 "REV3-like, catalytic subunit of DNA polymerase zeta (yeast)" 976 rs458017 REV3L 5980 6 111802784 NM_002912 NP_002903 C/T Y1078C plus 23497123 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.08 0.01 278 3 0.11 0 46 1 123 "by cluster,freq" radical 602776 6q21 "REV3-like, catalytic subunit of DNA polymerase zeta (yeast)" 977 rs459102 U2AF1L1 7310 5 112256664 NM_005083 NP_005074 G/T Q477K minus 1998865 1303 SEQUENOM CEPH CEPH (92) 92 0.26 0.26 0 92 1 106 "by doubleHit,submitter,freq" moderately conservative 601079 5q22 U2(RNU2) small nuclear RNA auxillary factor 1-like 1 978 rs459552 APC 324 5 112204655 NM_000038 NP_000029 A/T V1822D minus 620343 1303 SEQUENOM CEPH CEPH (92) 92 0.14 0.13 0.05 188 3 0.12 0.07 94 2 123 "by doubleHit,submitter,freq,cluster" radical 175100 5q21-q22 adenomatosis polyposis coli 979 rs459552 APC 324 5 112204655 NM_000038 NP_000029 A/T V1822D minus 3177080 619 WICVAR MITOGPOP6 CORIELL Mixed 48 0.17 0.13 0.05 188 3 0.12 0.07 94 2 123 "by doubleHit,submitter,freq,cluster" radical 175100 5q21-q22 adenomatosis polyposis coli 980 rs459552 APC 324 5 112204655 NM_000038 NP_000029 A/T V1822D minus 23991403 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.13 0.05 188 3 0.12 0.07 94 2 123 "by doubleHit,submitter,freq,cluster" radical 175100 5q21-q22 adenomatosis polyposis coli 981 rs462779 REV3L 5980 6 111802580 NM_002912 NP_002903 C/T T1146I minus 626446 1303 SEQUENOM CEPH CEPH (92) 92 0.23 0.31 0.13 284 3 0.45 0.05 70 2 123 "by doubleHit,freq,cluster" moderately conservative 602776 6q21 "REV3-like, catalytic subunit of DNA polymerase zeta (yeast)" 982 rs462779 REV3L 5980 6 111802580 NM_002912 NP_002903 C/T T1146I minus 4479749 506 NCBI NIHPDR NIHPDR 144 0.41 0.31 0.13 284 3 0.45 0.05 70 2 123 "by doubleHit,freq,cluster" moderately conservative 602776 6q21 "REV3-like, catalytic subunit of DNA polymerase zeta (yeast)" 983 rs462779 REV3L 5980 6 111802580 NM_002912 NP_002903 C/T T1146I minus 24038973 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.31 0.13 284 3 0.45 0.05 70 2 123 "by doubleHit,freq,cluster" moderately conservative 602776 6q21 "REV3-like, catalytic subunit of DNA polymerase zeta (yeast)" 984 rs470428 HP 3240 16 70652183 NM_005143 NP_005134 C/T T372A minus 757475 1303 SEQUENOM CEPH CEPH (92) 92 0.1 0.1 0 92 1 83 by freq Benign 0.039 34 Tolerant 1 2.81 50 moderately conservative 140100 16q22.1 haptoglobin 985 rs473267 PGM3 5238 6 83936886 NM_015599 NP_056414 C/T D466N plus 1383970 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 84 0.25 0.24 0.05 224 3 0.36 0.1 262 4 123 "by doubleHit,submitter,freq,cluster" Possibly damaging 1.614 9 Tolerant 0.48 2.78 20 conservative 172100 6q14.1-q15 phosphoglucomutase 3 986 rs473267 PGM3 5238 6 83936886 NM_015599 NP_056414 C/T D466N plus 1383970 1303 SEQUENOM CEPH CEPH (92) 92 0.2 0.24 0.05 224 3 0.36 0.1 262 4 123 "by doubleHit,submitter,freq,cluster" Possibly damaging 1.614 9 Tolerant 0.48 2.78 20 conservative 172100 6q14.1-q15 phosphoglucomutase 3 987 rs473267 PGM3 5238 6 83936886 NM_015599 NP_056414 C/T D466N plus 23404224 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.31 0.24 0.05 224 3 0.36 0.1 262 4 123 "by doubleHit,submitter,freq,cluster" Possibly damaging 1.614 9 Tolerant 0.48 2.78 20 conservative 172100 6q14.1-q15 phosphoglucomutase 3 988 rs475002 SNAPC2 6618 19 7892638 NM_003083 NP_003074 C/G L118V minus 644418 885 TSC-CSHL HapMap-CEPH-30-trios 116 0.44 0.45 0.09 267 4 0.31 0.01 42 2 121 "HapMap,doubleHit,freq" conservative 605076 19p13.3-p13.2 "small nuclear RNA activating complex, polypeptide 2, 45kDa" 989 rs475002 SNAPC2 6618 19 7892638 NM_003083 NP_003074 C/G L118V minus 644418 1303 SEQUENOM CEPH CEPH (92) 92 0.48 0.45 0.09 267 4 0.31 0.01 42 2 121 "HapMap,doubleHit,freq" conservative 605076 19p13.3-p13.2 "small nuclear RNA activating complex, polypeptide 2, 45kDa" 990 rs475002 SNAPC2 6618 19 7892638 NM_003083 NP_003074 C/G L118V minus 980252 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.14 0.45 0.09 267 4 0.31 0.01 42 2 121 "HapMap,doubleHit,freq" conservative 605076 19p13.3-p13.2 "small nuclear RNA activating complex, polypeptide 2, 45kDa" 991 rs475002 SNAPC2 6618 19 7892638 NM_003083 NP_003074 C/G L118V minus 980252 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 45 0.5 0.45 0.09 267 4 0.31 0.01 42 2 121 "HapMap,doubleHit,freq" conservative 605076 19p13.3-p13.2 "small nuclear RNA activating complex, polypeptide 2, 45kDa" 992 rs477207 AOC3 8639 17 38261899 NM_003734 NP_003725 C/T G700S minus 646683 687 TSC-SANGER SC_12_CA CEPH Caucasians (12) 11 0.5 0.5 0 17 2 0.31 0.14 121 5 119 "by cluster,freq" Benign 0.318 14 Tolerant 0.47 2.82 27 moderately conservative 603735 17q21 "amine oxidase, copper containing 3 (vascular adhesion protein 1)" 993 rs477207 AOC3 8639 17 38261899 NM_003734 NP_003725 C/T G700S minus 646683 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 6 0.5 0.5 0 17 2 0.31 0.14 121 5 119 "by cluster,freq" Benign 0.318 14 Tolerant 0.47 2.82 27 moderately conservative 603735 17q21 "amine oxidase, copper containing 3 (vascular adhesion protein 1)" 994 rs479632 PITX1 5307 5 134392417 NM_002653 NP_002644 C/G G299A minus 649161 1303 SEQUENOM CEPH CEPH (92) 92 0.47 0.47 0 92 1 100 "by doubleHit,freq,cluster" Benign 0.333 40 moderately conservative 602149 5q31 paired-like homeodomain transcription factor 1 995 rs482912 LAMP3 27074 3 184336372 NM_014398 NP_055213 A/G I318V minus 652506 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 16 0.31 0.31 0.06 184 3 0.39 0.03 1616 5 123 "HapMap,doubleHit,freq,cluster" Tolerant 1 2.75 25 conservative 605883 3q26.3-q27 lysosomal-associated membrane protein 3 996 rs482912 LAMP3 27074 3 184336372 NM_014398 NP_055213 A/G I318V minus 652506 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.34 0.31 0.06 184 3 0.39 0.03 1616 5 123 "HapMap,doubleHit,freq,cluster" Tolerant 1 2.75 25 conservative 605883 3q26.3-q27 lysosomal-associated membrane protein 3 997 rs482912 LAMP3 27074 3 184336372 NM_014398 NP_055213 A/G I318V minus 23973747 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.23 0.31 0.06 184 3 0.39 0.03 1616 5 123 "HapMap,doubleHit,freq,cluster" Tolerant 1 2.75 25 conservative 605883 3q26.3-q27 lysosomal-associated membrane protein 3 998 rs486055 MMP10 4319 11 102155634 NM_002425 NP_002416 C/T R53K plus 655712 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 10 0.2 0.14 0.06 150 3 0.02 0 46 1 123 by freq Benign 0.463 26 Tolerant 1 2.83 57 conservative 185260 11q22.3 matrix metalloproteinase 10 (stromelysin 2) 999 rs486055 MMP10 4319 11 102155634 NM_002425 NP_002416 C/T R53K plus 655712 1303 SEQUENOM CEPH CEPH (92) 92 0.1 0.14 0.06 150 3 0.02 0 46 1 123 by freq Benign 0.463 26 Tolerant 1 2.83 57 conservative 185260 11q22.3 matrix metalloproteinase 10 (stromelysin 2) 1000 rs486055 MMP10 4319 11 102155634 NM_002425 NP_002416 C/T R53K plus 24531742 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.14 0.06 150 3 0.02 0 46 1 123 by freq Benign 0.463 26 Tolerant 1 2.83 57 conservative 185260 11q22.3 matrix metalloproteinase 10 (stromelysin 2) 1001 rs486907 RNASEL 6041 1 179286214 NM_021133 NP_066956 A/G R462Q minus 12675607 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.44 0.46 0.02 154 2 0.27 0.05 346 4 118 "by doubleHit,submitter,freq,cluster" Borderline 1.218 5 Tolerant 0.6 3.15 28 conservative 180435 1q25 "ribonuclease L (2',5'-oligoisoadenylate synthetase-dependent)" 1002 rs486907 RNASEL 6041 1 179286214 NM_021133 NP_066956 A/G R462Q minus 12675607 1303 SEQUENOM CEPH CEPH (92) 92 0.47 0.46 0.02 154 2 0.27 0.05 346 4 118 "by doubleHit,submitter,freq,cluster" Borderline 1.218 5 Tolerant 0.6 3.15 28 conservative 180435 1q25 "ribonuclease L (2',5'-oligoisoadenylate synthetase-dependent)" 1003 rs487989 POLA2 23649 11 64821266 NM_002689 NP_002680 A/G G583R plus 657678 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 24 0.13 0.09 0.02 236 3 0.13 0.08 40 2 111 "HapMap,doubleHit,freq" Borderline 1.186 8 Borderline 0.2 2.98 12 moderately radical 11q13.1 "polymerase (DNA-directed), alpha (70kD)" 1004 rs487989 POLA2 23649 11 64821266 NM_002689 NP_002680 A/G G583R plus 657678 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 94 0.07 0.09 0.02 236 3 0.13 0.08 40 2 111 "HapMap,doubleHit,freq" Borderline 1.186 8 Borderline 0.2 2.98 12 moderately radical 11q13.1 "polymerase (DNA-directed), alpha (70kD)" 1005 rs487989 POLA2 23649 11 64821266 NM_002689 NP_002680 A/G G583R plus 5350029 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.1 0.09 0.02 236 3 0.13 0.08 40 2 111 "HapMap,doubleHit,freq" Borderline 1.186 8 Borderline 0.2 2.98 12 moderately radical 11q13.1 "polymerase (DNA-directed), alpha (70kD)" 1006 rs500079 PPP1R15A 23645 19 54070806 NM_014330 NP_055145 C/T T597A minus 2132902 1303 SEQUENOM CEPH CEPH (92) 92 0.17 0.2 0.05 140 2 0.32 0.16 94 2 123 "by doubleHit,freq,cluster" moderately conservative 19q13.2 "protein phosphatase 1, regulatory (inhibitor) subunit 15A" 1007 rs500079 PPP1R15A 23645 19 54070806 NM_014330 NP_055145 C/T T597A minus 23812937 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.25 0.2 0.05 140 2 0.32 0.16 94 2 123 "by doubleHit,freq,cluster" moderately conservative 19q13.2 "protein phosphatase 1, regulatory (inhibitor) subunit 15A" 1008 rs504122 SPRY2 10253 13 79809526 NM_005842 NP_005833 C/T P106S minus 674139 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 5 0.5 0.22 0.15 469 6 0.23 0.23 114 3 123 "by doubleHit,submitter,freq,cluster" Benign 0.913 9 Borderline 0.15 2.94 24 moderately conservative 602466 13q22.2 sprouty homolog 2 (Drosophila) 1009 rs504122 SPRY2 10253 13 79809526 NM_005842 NP_005833 C/T P106S minus 674139 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 94 0.35 0.22 0.15 469 6 0.23 0.23 114 3 123 "by doubleHit,submitter,freq,cluster" Benign 0.913 9 Borderline 0.15 2.94 24 moderately conservative 602466 13q22.2 sprouty homolog 2 (Drosophila) 1010 rs504122 SPRY2 10253 13 79809526 NM_005842 NP_005833 C/T P106S minus 674139 1303 SEQUENOM CEPH CEPH (92) 92 0.36 0.22 0.15 469 6 0.23 0.23 114 3 123 "by doubleHit,submitter,freq,cluster" Benign 0.913 9 Borderline 0.15 2.94 24 moderately conservative 602466 13q22.2 sprouty homolog 2 (Drosophila) 1011 rs504122 SPRY2 10253 13 79809526 NM_005842 NP_005833 C/T P106S minus 3177960 619 WICVAR MITOGPOP6 CORIELL Mixed 46 0.28 0.22 0.15 469 6 0.23 0.23 114 3 123 "by doubleHit,submitter,freq,cluster" Benign 0.913 9 Borderline 0.15 2.94 24 moderately conservative 602466 13q22.2 sprouty homolog 2 (Drosophila) 1012 rs504122 SPRY2 10253 13 79809526 NM_005842 NP_005833 C/T P106S minus 23975354 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.25 0.22 0.15 469 6 0.23 0.23 114 3 123 "by doubleHit,submitter,freq,cluster" Benign 0.913 9 Borderline 0.15 2.94 24 moderately conservative 602466 13q22.2 sprouty homolog 2 (Drosophila) 1013 rs504122 SPRY2 10253 13 79809526 NM_005842 NP_005833 C/T P106S minus 24811651 1303 SEQUENOM CEPH CEPH (92) 184 0.06 0.22 0.15 469 6 0.23 0.23 114 3 123 "by doubleHit,submitter,freq,cluster" Benign 0.913 9 Borderline 0.15 2.94 24 moderately conservative 602466 13q22.2 sprouty homolog 2 (Drosophila) 1014 rs506504 CHEK1 1111 11 125030405 NM_001274 NP_001265 C/T I471V minus 12675356 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.06 0.07 0.01 110 2 0.03 0.02 346 4 123 "by doubleHit,freq,cluster" Benign 0.088 10 conservative 603078 11q24-q24 CHK1 checkpoint homolog (S. pombe) 1015 rs506504 CHEK1 1111 11 125030405 NM_001274 NP_001265 C/T I471V minus 24363886 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.07 0.01 110 2 0.03 0.02 346 4 123 "by doubleHit,freq,cluster" Benign 0.088 10 conservative 603078 11q24-q24 CHK1 checkpoint homolog (S. pombe) 1016 rs507879 CASP5 838 11 104383137 NM_004347 NP_004338 A/G T90A minus 677961 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.43 0.45 0.04 192 4 0.25 0.03 1132 3 123 "by doubleHit,freq,cluster" moderately conservative 602665 11q22.2-q22.3 "caspase 5, apoptosis-related cysteine protease" 1017 rs507879 CASP5 838 11 104383137 NM_004347 NP_004338 A/G T90A minus 677961 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 92 0.45 0.45 0.04 192 4 0.25 0.03 1132 3 123 "by doubleHit,freq,cluster" moderately conservative 602665 11q22.2-q22.3 "caspase 5, apoptosis-related cysteine protease" 1018 rs507879 CASP5 838 11 104383137 NM_004347 NP_004338 A/G T90A minus 2832698 1303 SEQUENOM CEPH CEPH (92) 46 0.5 0.45 0.04 192 4 0.25 0.03 1132 3 123 "by doubleHit,freq,cluster" moderately conservative 602665 11q22.2-q22.3 "caspase 5, apoptosis-related cysteine protease" 1019 rs507879 CASP5 838 11 104383137 NM_004347 NP_004338 A/G T90A minus 4403105 649 FHCRC POPU1 USA (20) 40 0.4 0.45 0.04 192 4 0.25 0.03 1132 3 123 "by doubleHit,freq,cluster" moderately conservative 602665 11q22.2-q22.3 "caspase 5, apoptosis-related cysteine protease" 1020 rs508405 CAPN13 92291 2 30892591 NM_144575 NP_653176 A/G A280T minus 24636906 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.33 0.33 0 48 1 0.12 0.07 94 2 123 "by submitter,freq,cluster" Potentially intolerant 0.06 3.03 62 moderately conservative 2p22-p21 calpain 13 1021 rs523104 CASP5 838 11 104374918 NM_004347 NP_004338 C/G L318V plus 16124289 1303 SEQUENOM CEPH CEPH (92) 92 0.36 0.39 0.07 140 2 0.31 0.04 92 2 123 "by doubleHit,freq,cluster" Benign 0.088 10 conservative 602665 11q22.2-q22.3 "caspase 5, apoptosis-related cysteine protease" 1022 rs523104 CASP5 838 11 104374918 NM_004347 NP_004338 C/G L318V plus 24610835 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.46 0.39 0.07 140 2 0.31 0.04 92 2 123 "by doubleHit,freq,cluster" Benign 0.088 10 conservative 602665 11q22.2-q22.3 "caspase 5, apoptosis-related cysteine protease" 1023 rs527221 DMPK 1760 19 50967816 NM_004409 NP_004400 C/G L423V plus 24109680 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.15 0.15 0 46 1 0.11 0.1 88 2 123 "by cluster,freq" Benign 0.058 17 Tolerant 0.51 2.8 48 conservative 605377 19q13.3 dystrophia myotonica-protein kinase 1024 rs532648 FOXN1 8456 17 23888429 NM_003593 NP_003584 C/G A599P minus 703214 1303 SEQUENOM CEPH CEPH (92) 92 0.27 0.27 0 92 1 0.23 0 1496 1 108 "by doubleHit,freq,cluster" conservative 600838 17q11-q12 forkhead box N1 1025 rs532964 DMGDH 29958 5 78376042 NM_013391 NP_037523 C/T S279P minus 24413460 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.44 0.44 0 48 1 0.28 0.02 94 2 123 "by doubleHit,submitter,freq,cluster" Benign 0.739 7 Tolerant 1 2.79 17 moderately conservative 605849 5q14.1 dimethylglycine dehydrogenase 1026 rs533617 APOB 338 2 21145624 NM_000384 NP_000375 C/T H1923R plus 704195 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.02 0.04 0.02 260 3 123 "HapMap,submitter,freq" conservative 107730 2p24-p23 apolipoprotein B (including Ag(x) antigen) 1027 rs533617 APOB 338 2 21145624 NM_000384 NP_000375 C/T H1923R plus 704195 1303 SEQUENOM CEPH CEPH (92) 92 0.06 0.04 0.02 260 3 123 "HapMap,submitter,freq" conservative 107730 2p24-p23 apolipoprotein B (including Ag(x) antigen) 1028 rs533617 APOB 338 2 21145624 NM_000384 NP_000375 C/T H1923R plus 24242187 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.04 0.02 260 3 123 "HapMap,submitter,freq" conservative 107730 2p24-p23 apolipoprotein B (including Ag(x) antigen) 1029 rs542998 RTN3 10313 11 63243962 NM_201428 NP_958831 C/T V452A plus 5561507 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.18 0.19 0.03 168 2 0.43 0 46 1 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 604249 11q13 reticulon 3 1030 rs542998 RTN3 10313 11 63243962 NM_201428 NP_958831 C/T V452A plus 23743402 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.23 0.19 0.03 168 2 0.43 0 46 1 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 604249 11q13 reticulon 3 1031 rs543355 LAMA1 284217 18 6948609 NM_005559 NP_005550 C/T T2611A plus 714130 1303 SEQUENOM CEPH CEPH (92) 92 0.01 0.01 0.01 140 2 0.2 0.26 94 2 123 "by doubleHit,submitter,freq,cluster" Tolerant 0.46 2.77 13 moderately conservative 150320 18p11.23 "laminin, alpha 1" 1032 rs543355 LAMA1 284217 18 6948609 NM_005559 NP_005550 C/T T2611A plus 23585775 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.01 0.01 140 2 0.2 0.26 94 2 123 "by doubleHit,submitter,freq,cluster" Tolerant 0.46 2.77 13 moderately conservative 150320 18p11.23 "laminin, alpha 1" 1033 rs543573 KIAA0625 23064 9 132232383 NM_015046 NP_055861 C/T I1386V plus 714352 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.1 0.12 0.04 168 2 0.27 0.02 1596 3 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 608465 9q34.3 senataxin 1034 rs543573 KIAA0625 23064 9 132232383 NM_015046 NP_055861 C/T I1386V plus 23435974 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.17 0.12 0.04 168 2 0.27 0.02 1596 3 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 608465 9q34.3 senataxin 1035 rs544641 ZBTB3 79842 11 62276141 NM_024784 NP_079060 C/G I574M minus 12161398 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.02 0.03 0.01 166 2 0.16 0.08 160 5 123 "HapMap,doubleHit,freq,cluster" conservative 11q12.3 zinc finger and BTB domain containing 3 1036 rs544641 ZBTB3 79842 11 62276141 NM_024784 NP_079060 C/G I574M minus 24183476 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.04 0.03 0.01 166 2 0.16 0.08 160 5 123 "HapMap,doubleHit,freq,cluster" conservative 11q12.3 zinc finger and BTB domain containing 3 1037 rs550252 TCEB3 6924 1 23824246 NM_003198 NP_003189 C/T A490V plus 721179 1303 SEQUENOM CEPH CEPH (92) 92 0.04 0.04 0 92 1 119 by freq Borderline 1.097 8 moderately conservative 600786 1p36.1 "transcription elongation factor B (SIII), polypeptide 3 (110kDa, elongin A)" 1038 rs553717 GPC5 2262 13 91143580 NM_004466 NP_004457 A/G A155V minus 724691 1303 SEQUENOM CEPH CEPH (92) 92 0.17 0.17 0 92 1 0.06 0.04 94 2 123 "by doubleHit,submitter,freq,cluster" Benign 0.937 5 Potentially intolerant 0.1 2.78 29 moderately conservative 602446 13q32 glypican 5 1039 rs554202 MOGAT2 80168 11 75106606 NM_025098 NP_079374 A/G M9V plus 1814968 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.37 0.4 0.07 166 2 0.21 0.04 1559 3 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.385 10 Tolerant 0.61 2.91 21 conservative 11q13.3 monoacylglycerol O-acyltransferase 2 1040 rs554202 MOGAT2 80168 11 75106606 NM_025098 NP_079374 A/G M9V plus 23681355 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.48 0.4 0.07 166 2 0.21 0.04 1559 3 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.385 10 Tolerant 0.61 2.91 21 conservative 11q13.3 monoacylglycerol O-acyltransferase 2 1041 rs554971 IL28A 282616 19 44451175 NM_172138 NP_742150 A/G T10M minus 725976 1303 SEQUENOM CEPH CEPH (92) 92 0.38 0.38 0 92 1 103 by freq moderately conservative 607401 19q13.13 "interleukin 28A (interferon, lambda 2)" 1042 rs556052 PPP1R15A 23645 19 54069248 NM_014330 NP_055145 C/G A316P minus 727083 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.3 0.3 0 118 1 0.13 0 1490 1 120 "HapMap,doubleHit,freq,cluster" conservative 19q13.2 "protein phosphatase 1, regulatory (inhibitor) subunit 15A" 1043 rs557806 PPP1R15A 23645 19 54069054 NM_014330 NP_055145 C/G R251P minus 728867 1303 SEQUENOM CEPH CEPH (92) 92 0.29 0.29 0 92 1 120 "by doubleHit,freq,cluster" Tolerant 0.28 3.14 12 moderately radical 19q13.2 "protein phosphatase 1, regulatory (inhibitor) subunit 15A" 1044 rs558614 LATS2 26524 13 20460948 NM_014572 NP_055387 C/T A324V minus 729690 1303 SEQUENOM CEPH CEPH (92) 92 0.09 0.09 0 92 1 121 "by doubleHit,freq,cluster" Benign 0.45 5 moderately conservative 604861 13q11-q12 "LATS, large tumor suppressor, homolog 2 (Drosophila)" 1045 rs560096 IGHMBP2 3508 11 68435538 NM_002180 NP_002171 C/T L201S plus 76795 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 82 0.07 0.18 0.12 486 8 0.44 0.05 1840 10 123 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.773 5 moderately radical 600502 11q13.2-q13.4 immunoglobulin mu binding protein 2 1046 rs560096 IGHMBP2 3508 11 68435538 NM_002180 NP_002171 C/T L201S plus 76795 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 22 0.23 0.18 0.12 486 8 0.44 0.05 1840 10 123 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.773 5 moderately radical 600502 11q13.2-q13.4 immunoglobulin mu binding protein 2 1047 rs560096 IGHMBP2 3508 11 68435538 NM_002180 NP_002171 C/T L201S plus 76795 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 86 0.13 0.18 0.12 486 8 0.44 0.05 1840 10 123 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.773 5 moderately radical 600502 11q13.2-q13.4 immunoglobulin mu binding protein 2 1048 rs560096 IGHMBP2 3508 11 68435538 NM_002180 NP_002171 C/T L201S plus 76795 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.13 0.18 0.12 486 8 0.44 0.05 1840 10 123 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.773 5 moderately radical 600502 11q13.2-q13.4 immunoglobulin mu binding protein 2 1049 rs560096 IGHMBP2 3508 11 68435538 NM_002180 NP_002171 C/T L201S plus 76795 902 AFFY Caucasian 24 0.04 0.18 0.12 486 8 0.44 0.05 1840 10 123 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.773 5 moderately radical 600502 11q13.2-q13.4 immunoglobulin mu binding protein 2 1050 rs560096 IGHMBP2 3508 11 68435538 NM_002180 NP_002171 C/T L201S plus 76795 904 AFFY CEPH 12 0.25 0.18 0.12 486 8 0.44 0.05 1840 10 123 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.773 5 moderately radical 600502 11q13.2-q13.4 immunoglobulin mu binding protein 2 1051 rs560096 IGHMBP2 3508 11 68435538 NM_002180 NP_002171 C/T L201S plus 76795 1303 SEQUENOM CEPH CEPH (92) 92 0.39 0.18 0.12 486 8 0.44 0.05 1840 10 123 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.773 5 moderately radical 600502 11q13.2-q13.4 immunoglobulin mu binding protein 2 1052 rs560096 IGHMBP2 3508 11 68435538 NM_002180 NP_002171 C/T L201S plus 24102663 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.17 0.18 0.12 486 8 0.44 0.05 1840 10 123 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.773 5 moderately radical 600502 11q13.2-q13.4 immunoglobulin mu binding protein 2 1053 rs560191 TP53BP1 7158 15 41555066 NM_005657 NP_005648 C/G D353E plus 731297 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 6 0.5 0.37 0.07 266 4 0.26 0.18 136 4 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 1 3.04 12 conservative 605230 15q15-q21 "tumor protein p53 binding protein, 1" 1054 rs560191 TP53BP1 7158 15 41555066 NM_005657 NP_005648 C/G D353E plus 14391011 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.31 0.37 0.07 266 4 0.26 0.18 136 4 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 1 3.04 12 conservative 605230 15q15-q21 "tumor protein p53 binding protein, 1" 1055 rs560191 TP53BP1 7158 15 41555066 NM_005657 NP_005648 C/G D353E plus 14391011 1303 SEQUENOM CEPH CEPH (92) 92 0.44 0.37 0.07 266 4 0.26 0.18 136 4 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 1 3.04 12 conservative 605230 15q15-q21 "tumor protein p53 binding protein, 1" 1056 rs560191 TP53BP1 7158 15 41555066 NM_005657 NP_005648 C/G D353E plus 23963802 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.35 0.37 0.07 266 4 0.26 0.18 136 4 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 1 3.04 12 conservative 605230 15q15-q21 "tumor protein p53 binding protein, 1" 1057 rs562047 HSPA1A 3303 6 31891842 NM_005345 NP_005336 C/G E110D minus 3172585 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 52 0.04 0.06 0.01 236 2 123 "by doubleHit,freq,cluster" Benign 0.967 479 conservative 140550 6p21.3 heat shock 70kDa protein 1A 1058 rs562047 HSPA1A 3303 6 31891842 NM_005345 NP_005336 C/G E110D minus 24811755 1303 SEQUENOM CEPH CEPH (92) 184 0.06 0.06 0.01 236 2 123 "by doubleHit,freq,cluster" Benign 0.967 479 conservative 140550 6p21.3 heat shock 70kDa protein 1A 1059 rs564196 PPP1R15A 23645 19 54068394 NM_014330 NP_055145 C/T R31H minus 735374 1303 SEQUENOM CEPH CEPH (92) 92 0.46 0.46 0 92 1 120 "by doubleHit,freq,cluster" conservative 19q13.2 "protein phosphatase 1, regulatory (inhibitor) subunit 15A" 1060 rs566655 LAMA1 284217 18 7024508 NM_005559 NP_005550 A/C N674T minus 24554442 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.25 0.25 0 48 1 0.19 0.06 94 2 123 "by doubleHit,submitter,freq,cluster" Tolerant 1 2.85 10 moderately conservative 150320 18p11.23 "laminin, alpha 1" 1061 rs567083 MAK 4117 6 10883586 NM_005906 NP_005897 A/G P520S plus 738322 1303 SEQUENOM CEPH CEPH (92) 92 0.05 0.03 0.02 258 4 123 by freq Benign 0.546 14 moderately conservative 154235 6q22 male germ cell-associated kinase 1062 rs567083 MAK 4117 6 10883586 NM_005906 NP_005897 A/G P520S plus 2445066 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 24 0.04 0.03 0.02 258 4 123 by freq Benign 0.546 14 moderately conservative 154235 6q22 male germ cell-associated kinase 1063 rs567083 MAK 4117 6 10883586 NM_005906 NP_005897 A/G P520S plus 2445066 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 94 0.02 0.03 0.02 258 4 123 by freq Benign 0.546 14 moderately conservative 154235 6q22 male germ cell-associated kinase 1064 rs567083 MAK 4117 6 10883586 NM_005906 NP_005897 A/G P520S plus 24373650 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.03 0.02 258 4 123 by freq Benign 0.546 14 moderately conservative 154235 6q22 male germ cell-associated kinase 1065 rs569108 MS4A2 2206 11 59619680 NM_000139 NP_000130 C/T E237G minus 2390014 1303 SEQUENOM CEPH CEPH (92) 92 0.01 0.01 0 92 1 0.17 0 1092 1 100 "by cluster,freq" Probably damaging 2.009 6 moderately conservative 147138 11q13 "membrane-spanning 4-domains, subfamily A, member 2 (Fc fragment of IgE, high affinity I, receptor for; beta polypeptide)" 1066 rs573212 FBP2 8789 9 94429221 NM_003837 NP_003828 C/G V86L plus 16336543 902 AFFY Caucasian 22 0.09 0.15 0.04 80 3 0.13 0.11 150 4 123 "by submitter,freq,cluster" Borderline 1.205 53 Tolerant 1 2.79 82 conservative 603027 9q22.3 "fructose-1,6-bisphosphatase 2" 1067 rs573212 FBP2 8789 9 94429221 NM_003837 NP_003828 C/G V86L plus 16336543 904 AFFY CEPH 12 0.17 0.15 0.04 80 3 0.13 0.11 150 4 123 "by submitter,freq,cluster" Borderline 1.205 53 Tolerant 1 2.79 82 conservative 603027 9q22.3 "fructose-1,6-bisphosphatase 2" 1068 rs573212 FBP2 8789 9 94429221 NM_003837 NP_003828 C/G V86L plus 24071709 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.17 0.15 0.04 80 3 0.13 0.11 150 4 123 "by submitter,freq,cluster" Borderline 1.205 53 Tolerant 1 2.79 82 conservative 603027 9q22.3 "fructose-1,6-bisphosphatase 2" 1069 rs578430 MUSK 4593 9 110642698 NM_005592 NP_005583 G/T V829L plus 749904 1303 SEQUENOM CEPH CEPH (92) 92 0.07 0.07 0 92 1 123 by freq Benign 0.675 5 Tolerant 0.37 2.81 27 conservative 601296 9q31.3-q32 "muscle, skeletal, receptor tyrosine kinase" 1070 rs581157 IREM2 342510 17 70125184 NM_181449 NP_852114 G/T K19T plus 752704 885 TSC-CSHL HapMap-CEPH-30-trios 112 0.42 0.44 0.04 160 2 0.38 0.01 94 2 123 "HapMap,doubleHit,freq,cluster" moderately conservative 17q25.2 immune receptor expressed on myeloid cells 2 1071 rs581157 IREM2 342510 17 70125184 NM_181449 NP_852114 G/T K19T plus 24558713 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.48 0.44 0.04 160 2 0.38 0.01 94 2 123 "HapMap,doubleHit,freq,cluster" moderately conservative 17q25.2 immune receptor expressed on myeloid cells 2 1072 rs584367 PLA2G2D 26279 1 20187360 NM_012400 NP_036532 C/T S80G plus 1958114 1303 SEQUENOM CEPH CEPH (92) 92 0.22 0.3 0.16 140 2 0.3 0.05 1588 3 123 "by doubleHit,submitter,freq,cluster" Tolerant 0.37 2.8 179 moderately conservative 605630 1p36.12 "phospholipase A2, group IID" 1073 rs584367 PLA2G2D 26279 1 20187360 NM_012400 NP_036532 C/T S80G plus 24236283 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.46 0.3 0.16 140 2 0.3 0.05 1588 3 123 "by doubleHit,submitter,freq,cluster" Tolerant 0.37 2.8 179 moderately conservative 605630 1p36.12 "phospholipase A2, group IID" 1074 rs589623 DNCH2 79659 11 102587800 XM_370652 XP_370652 C/T R2871Q minus 23560235 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.23 0.23 0 48 1 0.25 0.11 94 2 123 "by doubleHit,submitter,freq,cluster" Tolerant 0.39 2.79 14 conservative 603297 11q21-q22.1 "dynein, cytoplasmic, heavy polypeptide 2" 1075 rs593818 CYP4F12 66002 19 15668884 NM_023944 NP_076433 A/G S522G plus 765638 1303 SEQUENOM CEPH CEPH (92) 92 0.49 0.44 0.09 140 2 0.36 0.13 94 2 123 "by doubleHit,freq,cluster" Benign 0.388 20 moderately conservative 19p13.1 "cytochrome P450, family 4, subfamily F, polypeptide 12" 1076 rs593818 CYP4F12 66002 19 15668884 NM_023944 NP_076433 A/G S522G plus 23580674 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.35 0.44 0.09 140 2 0.36 0.13 94 2 123 "by doubleHit,freq,cluster" Benign 0.388 20 moderately conservative 19p13.1 "cytochrome P450, family 4, subfamily F, polypeptide 12" 1077 rs597570 FEZ1 9638 11 124856682 NM_005103 NP_005094 A/T D123E minus 769458 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 10 0.2 0.22 0.08 358 5 0.1 0.03 1618 5 123 "HapMap,doubleHit,submitter,freq,cluster" Borderline 0.12 3.05 21 conservative 604825 11q24.2 fasciculation and elongation protein zeta 1 (zygin I) 1078 rs597570 FEZ1 9638 11 124856682 NM_005103 NP_005094 A/T D123E minus 769458 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 92 0.16 0.22 0.08 358 5 0.1 0.03 1618 5 123 "HapMap,doubleHit,submitter,freq,cluster" Borderline 0.12 3.05 21 conservative 604825 11q24.2 fasciculation and elongation protein zeta 1 (zygin I) 1079 rs597570 FEZ1 9638 11 124856682 NM_005103 NP_005094 A/T D123E minus 769458 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.17 0.22 0.08 358 5 0.1 0.03 1618 5 123 "HapMap,doubleHit,submitter,freq,cluster" Borderline 0.12 3.05 21 conservative 604825 11q24.2 fasciculation and elongation protein zeta 1 (zygin I) 1080 rs597570 FEZ1 9638 11 124856682 NM_005103 NP_005094 A/T D123E minus 16510765 1303 SEQUENOM CEPH CEPH (92) 92 0.34 0.22 0.08 358 5 0.1 0.03 1618 5 123 "HapMap,doubleHit,submitter,freq,cluster" Borderline 0.12 3.05 21 conservative 604825 11q24.2 fasciculation and elongation protein zeta 1 (zygin I) 1081 rs597570 FEZ1 9638 11 124856682 NM_005103 NP_005094 A/T D123E minus 23641456 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.2 0.22 0.08 358 5 0.1 0.03 1618 5 123 "HapMap,doubleHit,submitter,freq,cluster" Borderline 0.12 3.05 21 conservative 604825 11q24.2 fasciculation and elongation protein zeta 1 (zygin I) 1082 rs602990 VAV2 7410 9 133673548 NM_003371 NP_003362 C/T M584V plus 2835292 1303 SEQUENOM CEPH CEPH (92) 92 0.49 0.49 0 92 1 119 "by doubleHit,freq" Borderline 1.062 17 Tolerant 1 3.25 23 conservative 600428 9q34.1 vav 2 oncogene 1083 rs605059 HSD17B1 3292 17 37960432 NM_000413 NP_000404 C/T G313S minus 777110 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.43 0.29 0.05 162 3 0.36 0.04 48 2 121 "by doubleHit,freq,cluster" moderately conservative 109684 17q11-q21 hydroxysteroid (17-beta) dehydrogenase 1 1084 rs605059 HSD17B1 3292 17 37960432 NM_000413 NP_000404 C/T G313S minus 3176234 619 WICVAR MITOGPOP6 CORIELL Mixed 56 0.29 0.29 0.05 162 3 0.36 0.04 48 2 121 "by doubleHit,freq,cluster" moderately conservative 109684 17q11-q21 hydroxysteroid (17-beta) dehydrogenase 1 1085 rs605059 HSD17B1 3292 17 37960432 NM_000413 NP_000404 C/T G313S minus 16745938 1303 SEQUENOM CEPH CEPH (92) 92 0.27 0.29 0.05 162 3 0.36 0.04 48 2 121 "by doubleHit,freq,cluster" moderately conservative 109684 17q11-q21 hydroxysteroid (17-beta) dehydrogenase 1 1086 rs607230 LAMA1 284217 18 6970523 NM_005559 NP_005550 C/T K2002E plus 779323 1303 SEQUENOM CEPH CEPH (92) 92 0.37 0.37 0 92 1 121 "by doubleHit,freq,cluster" Borderline 0.19 2.76 13 moderately conservative 150320 18p11.23 "laminin, alpha 1" 1087 rs607567 MICL 160364 12 10022951 NM_201625 NP_963919 A/C C71G minus 23786563 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.25 0.25 0 48 1 0.17 0.18 94 2 123 "by doubleHit,submitter,freq,cluster" radical 12p13.31 myeloid inhibitory C-type lectin-like receptor 1088 rs608433 ZNF236 7776 18 72740115 NM_007345 NP_031371 C/T I613V minus 780552 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.03 0.07 0.04 260 3 0.1 0 48 1 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 604760 18q22-q23 zinc finger protein 236 1089 rs608433 ZNF236 7776 18 72740115 NM_007345 NP_031371 C/T I613V minus 780552 1303 SEQUENOM CEPH CEPH (92) 92 0.11 0.07 0.04 260 3 0.1 0 48 1 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 604760 18q22-q23 zinc finger protein 236 1090 rs608433 ZNF236 7776 18 72740115 NM_007345 NP_031371 C/T I613V minus 24107976 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.07 0.04 260 3 0.1 0 48 1 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 604760 18q22-q23 zinc finger protein 236 1091 rs608620 PCSK7 9159 11 116582219 NM_004716 NP_004707 G/T L688V minus 4079307 1303 SEQUENOM CEPH CEPH (92) 92 0.33 0.33 0 92 1 113 "by doubleHit,freq" conservative 604872 11q23-q24 proprotein convertase subtilisin/kexin type 7 1092 rs609290 CYP4F12 66002 19 15650140 NM_023944 NP_076433 C/T I90V minus 781430 1303 SEQUENOM CEPH CEPH (92) 92 0.09 0.09 0 92 1 83 by freq Benign 0.134 40 conservative 19p13.1 "cytochrome P450, family 4, subfamily F, polypeptide 12" 1093 rs609636 CYP4F12 66002 19 15650098 NM_023944 NP_076433 C/T N76D minus 781784 1303 SEQUENOM CEPH CEPH (92) 92 0.11 0.11 0 92 1 83 by freq Benign 0.358 40 conservative 19p13.1 "cytochrome P450, family 4, subfamily F, polypeptide 12" 1094 rs610308 PPP1R15A 23645 19 54069131 NM_014330 NP_055145 C/T K277E minus 782465 1303 SEQUENOM CEPH CEPH (92) 92 0.22 0.22 0 92 1 0.12 0 1282 1 120 "by doubleHit,freq,cluster" moderately conservative 19q13.2 "protein phosphatase 1, regulatory (inhibitor) subunit 15A" 1095 rs611251 PPP1R15A 23645 19 54068898 NM_014330 NP_055145 A/G V199A minus 5163966 1303 SEQUENOM CEPH CEPH (92) 92 0.16 0.16 0 92 1 0.07 0 738 1 120 "by doubleHit,freq,cluster" moderately conservative 19q13.2 "protein phosphatase 1, regulatory (inhibitor) subunit 15A" 1096 rs615942 COASY 80347 17 37968330 NM_025233 NP_079509 G/T S55Y minus 2909636 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.39 0.37 0.05 254 3 0.46 0.04 1578 3 123 "HapMap,doubleHit,freq,cluster" Benign 0.461 7 moderately radical 17q12-q21 Coenzyme A synthase 1097 rs615942 COASY 80347 17 37968330 NM_025233 NP_079509 G/T S55Y minus 2909636 1303 SEQUENOM CEPH CEPH (92) 92 0.32 0.37 0.05 254 3 0.46 0.04 1578 3 123 "HapMap,doubleHit,freq,cluster" Benign 0.461 7 moderately radical 17q12-q21 Coenzyme A synthase 1098 rs615942 COASY 80347 17 37968330 NM_025233 NP_079509 G/T S55Y minus 24587840 1371 PERLEGEN AFD_EUR_PANEL European American (24) 44 0.41 0.37 0.05 254 3 0.46 0.04 1578 3 123 "HapMap,doubleHit,freq,cluster" Benign 0.461 7 moderately radical 17q12-q21 Coenzyme A synthase 1099 rs616114 MEP1B 4225 18 28051919 NM_005925 NP_005916 A/G P695L minus 788399 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.38 0.4 0.04 168 2 0.32 0.01 1580 3 123 "HapMap,submitter,freq,cluster" Possibly damaging 1.917 5 moderately conservative 600389 18q12.2-q12.3 "meprin A, beta" 1100 rs616114 MEP1B 4225 18 28051919 NM_005925 NP_005916 A/G P695L minus 24687373 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.44 0.4 0.04 168 2 0.32 0.01 1580 3 123 "HapMap,submitter,freq,cluster" Possibly damaging 1.917 5 moderately conservative 600389 18q12.2-q12.3 "meprin A, beta" 1101 rs619203 ROS1 6098 6 117728877 NM_002944 NP_002935 C/G S2229C minus 791558 1303 SEQUENOM CEPH CEPH (92) 92 0.19 0.19 0 134 2 0.16 0.04 94 2 123 "by doubleHit,freq,cluster" Probably damaging 2.424 5 Tolerant 0.24 3.24 56 moderately radical 165020 6q22 v-ros UR2 sarcoma virus oncogene homolog 1 (avian) 1102 rs619203 ROS1 6098 6 117728877 NM_002944 NP_002935 C/G S2229C minus 24370589 1371 PERLEGEN AFD_EUR_PANEL European American (24) 42 0.19 0.19 0 134 2 0.16 0.04 94 2 123 "by doubleHit,freq,cluster" Probably damaging 2.424 5 Tolerant 0.24 3.24 56 moderately radical 165020 6q22 v-ros UR2 sarcoma virus oncogene homolog 1 (avian) 1103 rs622082 IGHMBP2 3508 11 68460535 NM_002180 NP_002171 A/G T671A plus 3172863 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 54 0.3 0.3 0 54 1 0.21 0 1498 1 120 "by doubleHit,freq,cluster" Borderline 1.238 5 moderately conservative 600502 11q13.2-q13.4 immunoglobulin mu binding protein 2 1104 rs627441 DLAT 1737 11 111413372 NM_001931 NP_001922 A/G V318A minus 799946 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.26 0.31 0.08 212 2 120 "HapMap,doubleHit,submitter,freq" Benign 0.096 17 Tolerant 1 2.82 44 moderately conservative 608770 11q23.1 dihydrolipoamide S-acetyltransferase (E2 component of pyruvate dehydrogenase complex) 1105 rs627441 DLAT 1737 11 111413372 NM_001931 NP_001922 A/G V318A minus 799946 1303 SEQUENOM CEPH CEPH (92) 92 0.38 0.31 0.08 212 2 120 "HapMap,doubleHit,submitter,freq" Benign 0.096 17 Tolerant 1 2.82 44 moderately conservative 608770 11q23.1 dihydrolipoamide S-acetyltransferase (E2 component of pyruvate dehydrogenase complex) 1106 rs627928 RNASEL 6041 1 179282994 NM_021133 NP_066956 G/T D541E minus 19095328 1303 SEQUENOM CEPH CEPH (92) 92 0.4 0.4 0 92 1 121 "by doubleHit,submitter,freq,cluster" Borderline 1.098 5 Tolerant 0.63 3.15 30 conservative 180435 1q25 "ribonuclease L (2',5'-oligoisoadenylate synthetase-dependent)" 1107 rs629682 AOC3 8639 17 38257563 NM_003734 NP_003725 C/T W226X minus 802226 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 83 0.4 0.4 0 83 1 0.39 0.05 166 2 108 HapMap Probably damaging Intolerant radical 603735 17q21 "amine oxidase, copper containing 3 (vascular adhesion protein 1)" 1108 rs629849 IGF2R 3482 6 160464820 NM_000876 NP_000867 A/G R1619G plus 802398 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 86 0.06 0.13 0.05 522 5 0.17 0.03 1864 7 123 "by doubleHit,freq,cluster" Benign 0.565 17 moderately radical 147280 6q26 insulin-like growth factor 2 receptor 1109 rs629849 IGF2R 3482 6 160464820 NM_000876 NP_000867 A/G R1619G plus 959503 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.14 0.13 0.05 522 5 0.17 0.03 1864 7 123 "by doubleHit,freq,cluster" Benign 0.565 17 moderately radical 147280 6q26 insulin-like growth factor 2 receptor 1110 rs629849 IGF2R 3482 6 160464820 NM_000876 NP_000867 A/G R1619G plus 959503 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 182 0.16 0.13 0.05 522 5 0.17 0.03 1864 7 123 "by doubleHit,freq,cluster" Benign 0.565 17 moderately radical 147280 6q26 insulin-like growth factor 2 receptor 1111 rs629849 IGF2R 3482 6 160464820 NM_000876 NP_000867 A/G R1619G plus 8819763 775 SNP500CANCER CAUC1 Caucasian (31) 60 0.2 0.13 0.05 522 5 0.17 0.03 1864 7 123 "by doubleHit,freq,cluster" Benign 0.565 17 moderately radical 147280 6q26 insulin-like growth factor 2 receptor 1112 rs629849 IGF2R 3482 6 160464820 NM_000876 NP_000867 A/G R1619G plus 12585908 693 EGP_SNPS PDR90 NIHPDR 180 0.11 0.13 0.05 522 5 0.17 0.03 1864 7 123 "by doubleHit,freq,cluster" Benign 0.565 17 moderately radical 147280 6q26 insulin-like growth factor 2 receptor 1113 rs629976 IL28B 282617 19 44427365 NM_172139 NP_742151 A/G R28H minus 802528 1303 SEQUENOM CEPH CEPH (92) 92 0.35 0.35 0 92 1 103 by freq conservative 607402 19q13.13 "interleukin 28B (interferon, lambda 3)" 1114 rs630079 AOC3 8639 17 38257494 NM_003734 NP_003725 C/T H203R minus 3311445 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 83 0.42 0.38 0.04 267 2 0.37 0 166 2 123 by freq Benign 0.618 13 Tolerant 0.6 2.9 22 conservative 603735 17q21 "amine oxidase, copper containing 3 (vascular adhesion protein 1)" 1115 rs630079 AOC3 8639 17 38257494 NM_003734 NP_003725 C/T H203R minus 24796535 1303 SEQUENOM CEPH CEPH (92) 184 0.36 0.38 0.04 267 2 0.37 0 166 2 123 by freq Benign 0.618 13 Tolerant 0.6 2.9 22 conservative 603735 17q21 "amine oxidase, copper containing 3 (vascular adhesion protein 1)" 1116 rs637186 CD5 921 11 60649182 NM_014207 NP_055022 A/G H461R plus 809905 1303 SEQUENOM CEPH CEPH (92) 92 0.2 0.15 0.11 140 2 0.02 0 46 1 123 "by doubleHit,submitter,freq,cluster" Benign 0.289 7 conservative 153340 11q13 CD5 antigen (p56-62) 1117 rs637186 CD5 921 11 60649182 NM_014207 NP_055022 A/G H461R plus 24569935 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.15 0.11 140 2 0.02 0 46 1 123 "by doubleHit,submitter,freq,cluster" Benign 0.289 7 conservative 153340 11q13 CD5 antigen (p56-62) 1118 rs638043 KRT2A 3849 12 51330534 NM_000423 NP_000414 C/T G219D plus 2200757 1303 SEQUENOM CEPH CEPH (92) 92 0.2 0.18 0.05 138 2 0.04 0.04 90 2 123 by freq Benign 0.91 152 Tolerant 0.32 2.93 110 moderately conservative 600194 12q11-q13 keratin 2A (epidermal ichthyosis bullosa of Siemens) 1119 rs638043 KRT2A 3849 12 51330534 NM_000423 NP_000414 C/T G219D plus 24388531 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.13 0.18 0.05 138 2 0.04 0.04 90 2 123 by freq Benign 0.91 152 Tolerant 0.32 2.93 110 moderately conservative 600194 12q11-q13 keratin 2A (epidermal ichthyosis bullosa of Siemens) 1120 rs641153 BF 629 6 32022159 NM_001710 NP_001701 C/T R32Q minus 5606986 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 28 0.11 0.14 0.06 350 4 0.27 0 96 2 123 "by doubleHit,freq,cluster" conservative 138470 6p21.3 "B-factor, properdin" 1121 rs641153 BF 629 6 32022159 NM_001710 NP_001701 C/T R32Q minus 5606986 1303 SEQUENOM CEPH CEPH (92) 92 0.22 0.14 0.06 350 4 0.27 0 96 2 123 "by doubleHit,freq,cluster" conservative 138470 6p21.3 "B-factor, properdin" 1122 rs641153 BF 629 6 32022159 NM_001710 NP_001701 C/T R32Q minus 12674483 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.11 0.14 0.06 350 4 0.27 0 96 2 123 "by doubleHit,freq,cluster" conservative 138470 6p21.3 "B-factor, properdin" 1123 rs641153 BF 629 6 32022159 NM_001710 NP_001701 C/T R32Q minus 24796283 1303 SEQUENOM CEPH CEPH (92) 184 0.11 0.14 0.06 350 4 0.27 0 96 2 123 "by doubleHit,freq,cluster" conservative 138470 6p21.3 "B-factor, properdin" 1124 rs648802 PERP 64065 6 138455026 NM_022121 NP_071404 C/G P143R plus 3070296 1303 SEQUENOM CEPH CEPH (92) 92 0.49 0.49 0 92 1 120 "by doubleHit,submitter,freq,cluster" Tolerant 0.91 3.19 11 moderately radical 6q24 "PERP, TP53 apoptosis effector" 1125 rs649224 ME2 4200 18 46712660 NM_002396 NP_002387 C/T G450E minus 822148 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.03 0.14 0.17 210 2 116 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.055 32 Tolerant 1 2.76 89 moderately conservative 154270 18q21 "malic enzyme 2, NAD(+)-dependent, mitochondrial" 1126 rs649224 ME2 4200 18 46712660 NM_002396 NP_002387 C/T G450E minus 822148 1303 SEQUENOM CEPH CEPH (92) 92 0.27 0.14 0.17 210 2 116 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.055 32 Tolerant 1 2.76 89 moderately conservative 154270 18q21 "malic enzyme 2, NAD(+)-dependent, mitochondrial" 1127 rs662471 LAMA1 284217 18 6998591 NM_005559 NP_005550 A/G M1340V minus 3086161 1303 SEQUENOM CEPH CEPH (92) 92 0.2 0.2 0 92 1 120 "by doubleHit,freq,cluster" Intolerant 0.04 2.76 13 conservative 150320 18p11.23 "laminin, alpha 1" 1128 rs663227 UNC93A 54346 6 167699136 NM_018974 NP_061847 C/T Y387H plus 836450 1303 SEQUENOM CEPH CEPH (92) 92 0.32 0.32 0 92 1 83 by freq Possibly damaging 1.716 5 Intolerant 0 2.78 21 moderately conservative 607995 6q27 unc-93 homolog A (C. elegans) 1129 rs663606 UNC93A 54346 6 167699185 NM_018974 NP_061847 C/T M403T plus 836836 1303 SEQUENOM CEPH CEPH (92) 92 0.46 0.46 0 92 1 121 "by submitter,freq,cluster" Benign 0.291 5 Tolerant 1 2.78 21 moderately conservative 607995 6q27 unc-93 homolog A (C. elegans) 1130 rs671871 LAMA1 284217 18 6967844 NM_005559 NP_005550 A/G I2076T plus 845270 1303 SEQUENOM CEPH CEPH (92) 92 0.02 0.09 0.13 140 2 0.22 0.11 94 2 123 "by doubleHit,submitter,freq,cluster" Borderline 0.2 2.76 13 moderately conservative 150320 18p11.23 "laminin, alpha 1" 1131 rs671871 LAMA1 284217 18 6967844 NM_005559 NP_005550 A/G I2076T plus 23585965 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.09 0.13 140 2 0.22 0.11 94 2 123 "by doubleHit,submitter,freq,cluster" Borderline 0.2 2.76 13 moderately conservative 150320 18p11.23 "laminin, alpha 1" 1132 rs676210 APOB 338 2 21143176 NM_000384 NP_000375 A/G P2739L plus 2152529 1303 SEQUENOM CEPH CEPH (92) 92 0.2 0.2 0.01 154 2 0.27 0.09 438 5 121 "by doubleHit,freq,cluster" moderately conservative 107730 2p24-p23 apolipoprotein B (including Ag(x) antigen) 1133 rs676210 APOB 338 2 21143176 NM_000384 NP_000375 A/G P2739L plus 8819681 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.19 0.2 0.01 154 2 0.27 0.09 438 5 121 "by doubleHit,freq,cluster" moderately conservative 107730 2p24-p23 apolipoprotein B (including Ag(x) antigen) 1134 rs676314 NAPSA 9476 19 55557347 NM_004851 NP_004842 C/T I40T minus 849807 1303 SEQUENOM CEPH CEPH (92) 92 0.25 0.25 0 92 1 120 "by doubleHit,submitter,freq,cluster" Benign 0.332 6 Tolerant 0.67 2.8 67 moderately conservative 605631 19q13.33 napsin A aspartic peptidase 1135 rs676823 GPR109A 338442 12 121712119 NM_177551 NP_808219 C/T F198L minus 850328 1303 SEQUENOM CEPH CEPH (92) 92 0.13 0.13 0 92 1 0.44 0 1496 1 123 "by cluster,freq" Tolerant 1 2.81 27 conservative 12q24.31 G protein-coupled receptor 109A 1136 rs679620 MMP3 4314 11 102218830 NM_002422 NP_002413 A/G K45E minus 4251046 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.33 0.38 0.05 306 4 0.33 0.03 1604 4 123 "HapMap,doubleHit,freq,cluster" Benign 0.012 45 Tolerant 1 2.72 58 moderately conservative 185250 11q22.3 "matrix metalloproteinase 3 (stromelysin 1, progelatinase)" 1137 rs679620 MMP3 4314 11 102218830 NM_002422 NP_002413 A/G K45E minus 4251046 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.43 0.38 0.05 306 4 0.33 0.03 1604 4 123 "HapMap,doubleHit,freq,cluster" Benign 0.012 45 Tolerant 1 2.72 58 moderately conservative 185250 11q22.3 "matrix metalloproteinase 3 (stromelysin 1, progelatinase)" 1138 rs679620 MMP3 4314 11 102218830 NM_002422 NP_002413 A/G K45E minus 4251046 1303 SEQUENOM CEPH CEPH (92) 92 0.36 0.38 0.05 306 4 0.33 0.03 1604 4 123 "HapMap,doubleHit,freq,cluster" Benign 0.012 45 Tolerant 1 2.72 58 moderately conservative 185250 11q22.3 "matrix metalloproteinase 3 (stromelysin 1, progelatinase)" 1139 rs679620 MMP3 4314 11 102218830 NM_002422 NP_002413 A/G K45E minus 24073656 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.33 0.38 0.05 306 4 0.33 0.03 1604 4 123 "HapMap,doubleHit,freq,cluster" Benign 0.012 45 Tolerant 1 2.72 58 moderately conservative 185250 11q22.3 "matrix metalloproteinase 3 (stromelysin 1, progelatinase)" 1140 rs679899 APOB 338 2 21162566 NM_000384 NP_000375 A/G A618V plus 2756662 1303 SEQUENOM CEPH CEPH (92) 92 0.49 0.49 0 92 1 0.26 0 94 1 121 "by doubleHit,freq,cluster" moderately conservative 107730 2p24-p23 apolipoprotein B (including Ag(x) antigen) 1141 rs682632 TEK 7010 9 27173463 NM_000459 NP_000450 G/T Q346P minus 1651479 1303 SEQUENOM CEPH CEPH (92) 92 0.02 0.02 0 92 1 121 "by cluster,freq" Possibly damaging 1.679 9 moderately conservative 600221 9p21 "TEK tyrosine kinase, endothelial (venous malformations, multiple cutaneous and mucosal)" 1142 rs684535 CDON 50937 11 125336180 NM_016952 NP_058648 A/T I1221N plus 858175 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.21 0.26 0.03 274 4 0.12 0.07 138 4 123 "HapMap,doubleHit,freq,cluster" moderately radical 608707 11q23-q24 cell adhesion molecule-related/down-regulated by oncogenes 1143 rs684535 CDON 50937 11 125336180 NM_016952 NP_058648 A/T I1221N plus 858175 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 92 0.25 0.26 0.03 274 4 0.12 0.07 138 4 123 "HapMap,doubleHit,freq,cluster" moderately radical 608707 11q23-q24 cell adhesion molecule-related/down-regulated by oncogenes 1144 rs684535 CDON 50937 11 125336180 NM_016952 NP_058648 A/T I1221N plus 858175 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.29 0.26 0.03 274 4 0.12 0.07 138 4 123 "HapMap,doubleHit,freq,cluster" moderately radical 608707 11q23-q24 cell adhesion molecule-related/down-regulated by oncogenes 1145 rs684535 CDON 50937 11 125336180 NM_016952 NP_058648 A/T I1221N plus 24597994 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.23 0.26 0.03 274 4 0.12 0.07 138 4 123 "HapMap,doubleHit,freq,cluster" moderately radical 608707 11q23-q24 cell adhesion molecule-related/down-regulated by oncogenes 1146 rs688906 DNCH2 79659 11 102534726 XM_370652 XP_370652 C/T K1413R minus 23559641 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.31 0.31 0 48 1 0.29 0.17 94 2 123 "by doubleHit,submitter,freq,cluster" Intolerant 0 2.81 12 conservative 603297 11q21-q22.1 "dynein, cytoplasmic, heavy polypeptide 2" 1147 rs689647 TP53BP1 7158 15 41549488 NM_005657 NP_005648 C/T G412S plus 863398 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.07 0.16 0.14 364 5 0.42 0.05 126 4 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 605230 15q15-q21 "tumor protein p53 binding protein, 1" 1148 rs689647 TP53BP1 7158 15 41549488 NM_005657 NP_005648 C/T G412S plus 863398 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 92 0.08 0.16 0.14 364 5 0.42 0.05 126 4 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 605230 15q15-q21 "tumor protein p53 binding protein, 1" 1149 rs689647 TP53BP1 7158 15 41549488 NM_005657 NP_005648 C/T G412S plus 10801045 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.07 0.16 0.14 364 5 0.42 0.05 126 4 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 605230 15q15-q21 "tumor protein p53 binding protein, 1" 1150 rs689647 TP53BP1 7158 15 41549488 NM_005657 NP_005648 C/T G412S plus 10801045 1303 SEQUENOM CEPH CEPH (92) 92 0.37 0.16 0.14 364 5 0.42 0.05 126 4 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 605230 15q15-q21 "tumor protein p53 binding protein, 1" 1151 rs689647 TP53BP1 7158 15 41549488 NM_005657 NP_005648 C/T G412S plus 24038555 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.13 0.16 0.14 364 5 0.42 0.05 126 4 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 605230 15q15-q21 "tumor protein p53 binding protein, 1" 1152 rs696217 GHRL 51738 3 10306457 NM_016362 NP_057446 G/T L72M plus 1598058 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.08 0.08 0 118 1 0.19 0 1522 2 120 "HapMap,doubleHit,freq,cluster" Benign 0.985 16 Borderline 0.11 3.02 26 conservative 605353 3p26-p25 ghrelin precursor 1153 rs699664 GGCX 2677 2 85692194 NM_000821 NP_000812 A/G R325Q minus 81736 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 82 0.29 0.34 0.07 340 4 0.32 0.06 258 4 123 "HapMap,doubleHit,freq" Borderline 1.157 9 Tolerant 0.32 3.19 16 conservative 137167 2p12 gamma-glutamyl carboxylase 1154 rs699664 GGCX 2677 2 85692194 NM_000821 NP_000812 A/G R325Q minus 81736 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.43 0.34 0.07 340 4 0.32 0.06 258 4 123 "HapMap,doubleHit,freq" Borderline 1.157 9 Tolerant 0.32 3.19 16 conservative 137167 2p12 gamma-glutamyl carboxylase 1155 rs699664 GGCX 2677 2 85692194 NM_000821 NP_000812 A/G R325Q minus 81736 1303 SEQUENOM CEPH CEPH (92) 92 0.29 0.34 0.07 340 4 0.32 0.06 258 4 123 "HapMap,doubleHit,freq" Borderline 1.157 9 Tolerant 0.32 3.19 16 conservative 137167 2p12 gamma-glutamyl carboxylase 1156 rs699664 GGCX 2677 2 85692194 NM_000821 NP_000812 A/G R325Q minus 24169475 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.31 0.34 0.07 340 4 0.32 0.06 258 4 123 "HapMap,doubleHit,freq" Borderline 1.157 9 Tolerant 0.32 3.19 16 conservative 137167 2p12 gamma-glutamyl carboxylase 1157 rs699738 CD2 914 1 117023189 NM_001767 NP_001758 G/T H266Q minus 3172797 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 22 0.32 0.2 0.06 162 4 0.29 0 1252 1 123 "by doubleHit,freq,cluster" Probably damaging 2.426 8 conservative 186990 1p13 "CD2 antigen (p50), sheep red blood cell receptor" 1158 rs699738 CD2 914 1 117023189 NM_001767 NP_001758 G/T H266Q minus 4385082 649 FHCRC POPU1 USA (20) 12 0.1 0.2 0.06 162 4 0.29 0 1252 1 123 "by doubleHit,freq,cluster" Probably damaging 2.426 8 conservative 186990 1p13 "CD2 antigen (p50), sheep red blood cell receptor" 1159 rs699738 CD2 914 1 117023189 NM_001767 NP_001758 G/T H266Q minus 4385082 649 FHCRC POPU1 USA (20) 36 0.2 0.2 0.06 162 4 0.29 0 1252 1 123 "by doubleHit,freq,cluster" Probably damaging 2.426 8 conservative 186990 1p13 "CD2 antigen (p50), sheep red blood cell receptor" 1160 rs699738 CD2 914 1 117023189 NM_001767 NP_001758 G/T H266Q minus 17337954 1303 SEQUENOM CEPH CEPH (92) 92 0.18 0.2 0.06 162 4 0.29 0 1252 1 123 "by doubleHit,freq,cluster" Probably damaging 2.426 8 conservative 186990 1p13 "CD2 antigen (p50), sheep red blood cell receptor" 1161 rs700241 DAB2 1601 5 39412889 NM_001343 NP_001334 A/G T586I plus 2681857 885 TSC-CSHL HapMap-CEPH-30-trios 116 0.02 0.02 0 116 1 0.02 0 1498 1 108 "HapMap,freq,cluster" Benign 0.675 6 Potentially intolerant 0.06 3.14 33 moderately conservative 601236 5p13 "disabled homolog 2, mitogen-responsive phosphoprotein (Drosophila)" 1162 rs701753 CP 1356 3 150398933 NM_000096 NP_000087 A/T E544D plus 887587 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 10 0.2 0.08 0.03 222 3 0.21 0 14 1 123 "HapMap,freq,cluster" Potentially damaging 1.389 11 conservative 117700 3q23-q25 ceruloplasmin (ferroxidase) 1163 rs701753 CP 1356 3 150398933 NM_000096 NP_000087 A/T E544D plus 1914677 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.07 0.08 0.03 222 3 0.21 0 14 1 123 "HapMap,freq,cluster" Potentially damaging 1.389 11 conservative 117700 3q23-q25 ceruloplasmin (ferroxidase) 1164 rs701753 CP 1356 3 150398933 NM_000096 NP_000087 A/T E544D plus 1914677 1303 SEQUENOM CEPH CEPH (92) 92 0.09 0.08 0.03 222 3 0.21 0 14 1 123 "HapMap,freq,cluster" Potentially damaging 1.389 11 conservative 117700 3q23-q25 ceruloplasmin (ferroxidase) 1165 rs701865 PDE6C 5146 10 95371763 NM_006204 NP_006195 A/T S270T plus 1477173 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.43 0.44 0.01 256 3 0.42 0.08 84 2 123 "HapMap,doubleHit,submitter,freq,cluster" Borderline 1.051 41 Tolerant 0.81 2.86 45 moderately conservative 600827 10q24 "phosphodiesterase 6C, cGMP-specific, cone, alpha prime" 1166 rs701865 PDE6C 5146 10 95371763 NM_006204 NP_006195 A/T S270T plus 1477173 1303 SEQUENOM CEPH CEPH (92) 92 0.45 0.44 0.01 256 3 0.42 0.08 84 2 123 "HapMap,doubleHit,submitter,freq,cluster" Borderline 1.051 41 Tolerant 0.81 2.86 45 moderately conservative 600827 10q24 "phosphodiesterase 6C, cGMP-specific, cone, alpha prime" 1167 rs701865 PDE6C 5146 10 95371763 NM_006204 NP_006195 A/T S270T plus 23580834 1371 PERLEGEN AFD_EUR_PANEL European American (24) 44 0.43 0.44 0.01 256 3 0.42 0.08 84 2 123 "HapMap,doubleHit,submitter,freq,cluster" Borderline 1.051 41 Tolerant 0.81 2.86 45 moderately conservative 600827 10q24 "phosphodiesterase 6C, cGMP-specific, cone, alpha prime" 1168 rs702689 MAP3K1 4214 5 56213200 XM_042066 XP_042066 A/G D940N plus 1146310 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 84 0.19 0.24 0.1 333 5 0.33 0.09 430 6 123 "by doubleHit,submitter,freq,cluster" conservative 600982 5q11.2 mitogen-activated protein kinase kinase kinase 1 1169 rs702689 MAP3K1 4214 5 56213200 XM_042066 XP_042066 A/G D940N plus 3176945 619 WICVAR MITOGPOP6 CORIELL Mixed 25 0.5 0.24 0.1 333 5 0.33 0.09 430 6 123 "by doubleHit,submitter,freq,cluster" conservative 600982 5q11.2 mitogen-activated protein kinase kinase kinase 1 1170 rs702689 MAP3K1 4214 5 56213200 XM_042066 XP_042066 A/G D940N plus 3576043 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 84 0.19 0.24 0.1 333 5 0.33 0.09 430 6 123 "by doubleHit,submitter,freq,cluster" conservative 600982 5q11.2 mitogen-activated protein kinase kinase kinase 1 1171 rs702689 MAP3K1 4214 5 56213200 XM_042066 XP_042066 A/G D940N plus 3576043 1303 SEQUENOM CEPH CEPH (92) 92 0.21 0.24 0.1 333 5 0.33 0.09 430 6 123 "by doubleHit,submitter,freq,cluster" conservative 600982 5q11.2 mitogen-activated protein kinase kinase kinase 1 1172 rs702689 MAP3K1 4214 5 56213200 XM_042066 XP_042066 A/G D940N plus 23358119 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.33 0.24 0.1 333 5 0.33 0.09 430 6 123 "by doubleHit,submitter,freq,cluster" conservative 600982 5q11.2 mitogen-activated protein kinase kinase kinase 1 1173 rs707555 PCK1 5105 20 55571301 NM_002591 NP_002582 C/G V184L minus 1507075 1303 SEQUENOM CEPH CEPH (92) 92 0.11 0.11 0.01 140 2 0.15 0.18 94 2 123 "by doubleHit,submitter,freq,cluster" Potentially damaging 1.34 53 conservative 261680 20q13.31 phosphoenolpyruvate carboxykinase 1 (soluble) 1174 rs707555 PCK1 5105 20 55571301 NM_002591 NP_002582 C/G V184L minus 24006946 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.11 0.01 140 2 0.15 0.18 94 2 123 "by doubleHit,submitter,freq,cluster" Potentially damaging 1.34 53 conservative 261680 20q13.31 phosphoenolpyruvate carboxykinase 1 (soluble) 1175 rs707950 HLA-DQA1 3117 6 32717851 NM_002122 NP_002113 C/G Q152H plus 24816100 1303 SEQUENOM CEPH CEPH (92) 184 0.27 0.27 0 184 1 123 by freq Benign 0.479 191 Tolerant 0.97 2.84 306 conservative 146880 6p21.3 "major histocompatibility complex, class II, DQ alpha 1" 1176 rs709012 SN 6614 20 3623498 NM_023068 NP_075556 G/T H919P plus 8345514 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.42 0.42 0.07 214 3 0.23 0.02 1594 3 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.134 6 Tolerant 0.3 2.78 11 moderately conservative 600751 20p13 sialoadhesin 1177 rs709012 SN 6614 20 3623498 NM_023068 NP_075556 G/T H919P plus 8345514 1303 SEQUENOM CEPH CEPH (92) 46 0.5 0.42 0.07 214 3 0.23 0.02 1594 3 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.134 6 Tolerant 0.3 2.78 11 moderately conservative 600751 20p13 sialoadhesin 1178 rs709012 SN 6614 20 3623498 NM_023068 NP_075556 G/T H919P plus 24497001 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.33 0.42 0.07 214 3 0.23 0.02 1594 3 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.134 6 Tolerant 0.3 2.78 11 moderately conservative 600751 20p13 sialoadhesin 1179 rs709932 SERPINA1 5265 14 93918954 NM_000295 NP_000286 A/G R125H minus 1487247 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 82 0.17 0.15 0.06 502 7 0.09 0.09 279 5 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 0.39 2.75 79 conservative 107400 14q32.1 "serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1" 1180 rs709932 SERPINA1 5265 14 93918954 NM_000295 NP_000286 A/G R125H minus 1487247 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 22 0.09 0.15 0.06 502 7 0.09 0.09 279 5 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 0.39 2.75 79 conservative 107400 14q32.1 "serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1" 1181 rs709932 SERPINA1 5265 14 93918954 NM_000295 NP_000286 A/G R125H minus 1487247 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 94 0.11 0.15 0.06 502 7 0.09 0.09 279 5 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 0.39 2.75 79 conservative 107400 14q32.1 "serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1" 1182 rs709932 SERPINA1 5265 14 93918954 NM_000295 NP_000286 A/G R125H minus 1487247 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.14 0.15 0.06 502 7 0.09 0.09 279 5 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 0.39 2.75 79 conservative 107400 14q32.1 "serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1" 1183 rs709932 SERPINA1 5265 14 93918954 NM_000295 NP_000286 A/G R125H minus 1487247 1303 SEQUENOM CEPH CEPH (92) 92 0.15 0.15 0.06 502 7 0.09 0.09 279 5 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 0.39 2.75 79 conservative 107400 14q32.1 "serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1" 1184 rs709932 SERPINA1 5265 14 93918954 NM_000295 NP_000286 A/G R125H minus 3177172 619 WICVAR MITOGPOP6 CORIELL Mixed 44 0.32 0.15 0.06 502 7 0.09 0.09 279 5 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 0.39 2.75 79 conservative 107400 14q32.1 "serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1" 1185 rs709932 SERPINA1 5265 14 93918954 NM_000295 NP_000286 A/G R125H minus 24129851 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.15 0.06 502 7 0.09 0.09 279 5 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 0.39 2.75 79 conservative 107400 14q32.1 "serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1" 1186 rs710187 GCAT 23464 22 36528589 NM_014291 NP_055106 C/T R39C plus 137242 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 12 0.42 0.47 0.01 224 3 0.26 0.06 34 2 123 "HapMap,doubleHit,freq,cluster" Probably damaging 2.278 7 Intolerant 0 2.8 77 radical 607422 22q13.1 glycine C-acetyltransferase (2-amino-3-ketobutyrate coenzyme A ligase) 1187 rs710187 GCAT 23464 22 36528589 NM_014291 NP_055106 C/T R39C plus 7997788 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.47 0.47 0.01 224 3 0.26 0.06 34 2 123 "HapMap,doubleHit,freq,cluster" Probably damaging 2.278 7 Intolerant 0 2.8 77 radical 607422 22q13.1 glycine C-acetyltransferase (2-amino-3-ketobutyrate coenzyme A ligase) 1188 rs710187 GCAT 23464 22 36528589 NM_014291 NP_055106 C/T R39C plus 7997788 1303 SEQUENOM CEPH CEPH (92) 92 0.47 0.47 0.01 224 3 0.26 0.06 34 2 123 "HapMap,doubleHit,freq,cluster" Probably damaging 2.278 7 Intolerant 0 2.8 77 radical 607422 22q13.1 glycine C-acetyltransferase (2-amino-3-ketobutyrate coenzyme A ligase) 1189 rs710193 ST13 6767 22 39547690 NM_003932 NP_003923 C/T M297I plus 2671357 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 84 0.15 0.15 0 84 1 0.05 0 168 2 92 "by doubleHit,freq" Benign 0.952 7 Potentially intolerant 0.1 3.06 19 conservative 606796 22q13.2 suppression of tumorigenicity 13 (colon carcinoma) (Hsp70 interacting protein) 1190 rs712665 U2AF1L1 7310 5 112255698 NM_005083 NP_005074 C/T S155G minus 1998868 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.38 0.3 0.09 260 3 0.15 0.06 1588 3 123 "HapMap,doubleHit,submitter,freq,cluster" Possibly damaging 1.581 7 moderately conservative 601079 5q22 U2(RNU2) small nuclear RNA auxillary factor 1-like 1 1191 rs712665 U2AF1L1 7310 5 112255698 NM_005083 NP_005074 C/T S155G minus 1998868 1303 SEQUENOM CEPH CEPH (92) 92 0.21 0.3 0.09 260 3 0.15 0.06 1588 3 123 "HapMap,doubleHit,submitter,freq,cluster" Possibly damaging 1.581 7 moderately conservative 601079 5q22 U2(RNU2) small nuclear RNA auxillary factor 1-like 1 1192 rs712665 U2AF1L1 7310 5 112255698 NM_005083 NP_005074 C/T S155G minus 23418318 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.29 0.3 0.09 260 3 0.15 0.06 1588 3 123 "HapMap,doubleHit,submitter,freq,cluster" Possibly damaging 1.581 7 moderately conservative 601079 5q22 U2(RNU2) small nuclear RNA auxillary factor 1-like 1 1193 rs714368 SLC22A16 85413 6 110884821 NM_033125 NP_149116 A/G H49R minus 10328090 1303 SEQUENOM CEPH CEPH (92) 92 0.19 0.24 0.11 140 2 0.39 0.02 92 2 123 "by doubleHit,submitter,freq,cluster" Possibly damaging 1.615 5 Potentially intolerant 0.07 2.78 19 conservative 608276 6q22.1 "solute carrier family 22 (organic cation transporter), member 16" 1194 rs714368 SLC22A16 85413 6 110884821 NM_033125 NP_149116 A/G H49R minus 23456009 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.35 0.24 0.11 140 2 0.39 0.02 92 2 123 "by doubleHit,submitter,freq,cluster" Possibly damaging 1.615 5 Potentially intolerant 0.07 2.78 19 conservative 608276 6q22.1 "solute carrier family 22 (organic cation transporter), member 16" 1195 rs721917 SFTPD 6441 10 81696304 NM_003019 NP_003010 C/T M31T minus 63537 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.43 0.43 0.04 336 5 0.41 0.04 1964 9 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 178635 10q22.2-q23.1 "surfactant, pulmonary-associated protein D" 1196 rs721917 SFTPD 6441 10 81696304 NM_003019 NP_003010 C/T M31T minus 63537 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.41 0.43 0.04 336 5 0.41 0.04 1964 9 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 178635 10q22.2-q23.1 "surfactant, pulmonary-associated protein D" 1197 rs721917 SFTPD 6441 10 81696304 NM_003019 NP_003010 C/T M31T minus 63537 1303 SEQUENOM CEPH CEPH (92) 92 0.49 0.43 0.04 336 5 0.41 0.04 1964 9 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 178635 10q22.2-q23.1 "surfactant, pulmonary-associated protein D" 1198 rs721917 SFTPD 6441 10 81696304 NM_003019 NP_003010 C/T M31T minus 8819859 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.4 0.43 0.04 336 5 0.41 0.04 1964 9 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 178635 10q22.2-q23.1 "surfactant, pulmonary-associated protein D" 1199 rs721917 SFTPD 6441 10 81696304 NM_003019 NP_003010 C/T M31T minus 23388886 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.42 0.43 0.04 336 5 0.41 0.04 1964 9 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 178635 10q22.2-q23.1 "surfactant, pulmonary-associated protein D" 1200 rs723077 TTC12 54970 11 112699378 NM_017868 NP_060338 A/C M73L plus 65174 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 82 0.48 0.46 0.03 486 8 0.29 0.19 203 6 123 "HapMap,doubleHit,submitter,freq" conservative 11q23.2 tetratricopeptide repeat domain 12 1201 rs723077 TTC12 54970 11 112699378 NM_017868 NP_060338 A/C M73L plus 65174 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.43 0.46 0.03 486 8 0.29 0.19 203 6 123 "HapMap,doubleHit,submitter,freq" conservative 11q23.2 tetratricopeptide repeat domain 12 1202 rs723077 TTC12 54970 11 112699378 NM_017868 NP_060338 A/C M73L plus 65174 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 90 0.47 0.46 0.03 486 8 0.29 0.19 203 6 123 "HapMap,doubleHit,submitter,freq" conservative 11q23.2 tetratricopeptide repeat domain 12 1203 rs723077 TTC12 54970 11 112699378 NM_017868 NP_060338 A/C M73L plus 65174 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.46 0.46 0.03 486 8 0.29 0.19 203 6 123 "HapMap,doubleHit,submitter,freq" conservative 11q23.2 tetratricopeptide repeat domain 12 1204 rs723077 TTC12 54970 11 112699378 NM_017868 NP_060338 A/C M73L plus 65174 902 AFFY Caucasian 24 0.38 0.46 0.03 486 8 0.29 0.19 203 6 123 "HapMap,doubleHit,submitter,freq" conservative 11q23.2 tetratricopeptide repeat domain 12 1205 rs723077 TTC12 54970 11 112699378 NM_017868 NP_060338 A/C M73L plus 65174 904 AFFY CEPH 40 0.43 0.46 0.03 486 8 0.29 0.19 203 6 123 "HapMap,doubleHit,submitter,freq" conservative 11q23.2 tetratricopeptide repeat domain 12 1206 rs723077 TTC12 54970 11 112699378 NM_017868 NP_060338 A/C M73L plus 65174 1303 SEQUENOM CEPH CEPH (92) 92 0.44 0.46 0.03 486 8 0.29 0.19 203 6 123 "HapMap,doubleHit,submitter,freq" conservative 11q23.2 tetratricopeptide repeat domain 12 1207 rs723077 TTC12 54970 11 112699378 NM_017868 NP_060338 A/C M73L plus 24565864 1371 PERLEGEN AFD_EUR_PANEL European American (24) 24 0.5 0.46 0.03 486 8 0.29 0.19 203 6 123 "HapMap,doubleHit,submitter,freq" conservative 11q23.2 tetratricopeptide repeat domain 12 1208 rs723685 SLC22A16 85413 6 110870568 NM_033125 NP_149116 C/T V252A minus 66006 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.08 0.06 0.04 210 2 121 "HapMap,doubleHit,freq,cluster" Potentially damaging 1.416 6 Intolerant 0.01 2.79 21 moderately conservative 608276 6q22.1 "solute carrier family 22 (organic cation transporter), member 16" 1209 rs723685 SLC22A16 85413 6 110870568 NM_033125 NP_149116 C/T V252A minus 66006 1303 SEQUENOM CEPH CEPH (92) 92 0.03 0.06 0.04 210 2 121 "HapMap,doubleHit,freq,cluster" Potentially damaging 1.416 6 Intolerant 0.01 2.79 21 moderately conservative 608276 6q22.1 "solute carrier family 22 (organic cation transporter), member 16" 1210 rs724558 SERPINB10 5273 18 59736240 NM_005024 NP_005015 C/T I99T plus 67221 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 82 0.18 0.15 0.04 630 7 0.29 0.13 304 6 123 "HapMap,doubleHit,freq,cluster" Potentially intolerant 0.07 2.76 59 moderately conservative 602058 18q21.3 "serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 10" 1211 rs724558 SERPINB10 5273 18 59736240 NM_005024 NP_005015 C/T I99T plus 67221 766 TSC-CSHL WICGR1_CAUCASIAN WICGR Caucasian (93) 94 0.14 0.15 0.04 630 7 0.29 0.13 304 6 123 "HapMap,doubleHit,freq,cluster" Potentially intolerant 0.07 2.76 59 moderately conservative 602058 18q21.3 "serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 10" 1212 rs724558 SERPINB10 5273 18 59736240 NM_005024 NP_005015 C/T I99T plus 67221 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.07 0.15 0.04 630 7 0.29 0.13 304 6 123 "HapMap,doubleHit,freq,cluster" Potentially intolerant 0.07 2.76 59 moderately conservative 602058 18q21.3 "serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 10" 1213 rs724558 SERPINB10 5273 18 59736240 NM_005024 NP_005015 C/T I99T plus 67221 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 180 0.09 0.15 0.04 630 7 0.29 0.13 304 6 123 "HapMap,doubleHit,freq,cluster" Potentially intolerant 0.07 2.76 59 moderately conservative 602058 18q21.3 "serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 10" 1214 rs724558 SERPINB10 5273 18 59736240 NM_005024 NP_005015 C/T I99T plus 67221 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.19 0.15 0.04 630 7 0.29 0.13 304 6 123 "HapMap,doubleHit,freq,cluster" Potentially intolerant 0.07 2.76 59 moderately conservative 602058 18q21.3 "serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 10" 1215 rs724558 SERPINB10 5273 18 59736240 NM_005024 NP_005015 C/T I99T plus 67221 1303 SEQUENOM CEPH CEPH (92) 92 0.16 0.15 0.04 630 7 0.29 0.13 304 6 123 "HapMap,doubleHit,freq,cluster" Potentially intolerant 0.07 2.76 59 moderately conservative 602058 18q21.3 "serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 10" 1216 rs724558 SERPINB10 5273 18 59736240 NM_005024 NP_005015 C/T I99T plus 23531843 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.19 0.15 0.04 630 7 0.29 0.13 304 6 123 "HapMap,doubleHit,freq,cluster" Potentially intolerant 0.07 2.76 59 moderately conservative 602058 18q21.3 "serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 10" 1217 rs731170 LILRB4 11006 19 59868074 NM_006847 NP_006838 A/G D223G plus 76395 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.34 0.26 0.14 306 5 0.22 0 1496 1 123 "HapMap,doubleHit,freq,cluster" Benign 0.193 27 moderately conservative 604821 19q13.4 "leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 4" 1218 rs731170 LILRB4 11006 19 59868074 NM_006847 NP_006838 A/G D223G plus 76395 1303 SEQUENOM CEPH CEPH (92) 92 0.11 0.26 0.14 306 5 0.22 0 1496 1 123 "HapMap,doubleHit,freq,cluster" Benign 0.193 27 moderately conservative 604821 19q13.4 "leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 4" 1219 rs731170 LILRB4 11006 19 59868074 NM_006847 NP_006838 A/G D223G plus 16359984 649 FHCRC POPU1 USA (20) 16 0.05 0.26 0.14 306 5 0.22 0 1496 1 123 "HapMap,doubleHit,freq,cluster" Benign 0.193 27 moderately conservative 604821 19q13.4 "leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 4" 1220 rs731170 LILRB4 11006 19 59868074 NM_006847 NP_006838 A/G D223G plus 16359984 649 FHCRC POPU1 USA (20) 38 0.35 0.26 0.14 306 5 0.22 0 1496 1 123 "HapMap,doubleHit,freq,cluster" Benign 0.193 27 moderately conservative 604821 19q13.4 "leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 4" 1221 rs731170 LILRB4 11006 19 59868074 NM_006847 NP_006838 A/G D223G plus 16360036 649 FHCRC POPU1 USA (20) 40 0.4 0.26 0.14 306 5 0.22 0 1496 1 123 "HapMap,doubleHit,freq,cluster" Benign 0.193 27 moderately conservative 604821 19q13.4 "leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 4" 1222 rs732774 ATP7B 540 13 51421809 NM_000053 NP_000044 A/G R952K minus 78425 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.36 0.47 0.03 274 4 0.38 0.08 130 4 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.137 20 Tolerant 0.99 2.94 20 conservative 606882 13q14.2-q21 "ATPase, Cu++ transporting, beta polypeptide (Wilson disease)" 1223 rs732774 ATP7B 540 13 51421809 NM_000053 NP_000044 A/G R952K minus 78425 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 92 0.48 0.47 0.03 274 4 0.38 0.08 130 4 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.137 20 Tolerant 0.99 2.94 20 conservative 606882 13q14.2-q21 "ATPase, Cu++ transporting, beta polypeptide (Wilson disease)" 1224 rs732774 ATP7B 540 13 51421809 NM_000053 NP_000044 A/G R952K minus 78425 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.49 0.47 0.03 274 4 0.38 0.08 130 4 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.137 20 Tolerant 0.99 2.94 20 conservative 606882 13q14.2-q21 "ATPase, Cu++ transporting, beta polypeptide (Wilson disease)" 1225 rs732774 ATP7B 540 13 51421809 NM_000053 NP_000044 A/G R952K minus 24448176 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.46 0.47 0.03 274 4 0.38 0.08 130 4 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.137 20 Tolerant 0.99 2.94 20 conservative 606882 13q14.2-q21 "ATPase, Cu++ transporting, beta polypeptide (Wilson disease)" 1226 rs733731 PGLYRP2 114770 19 15448185 NM_052890 NP_443122 A/G R99Q minus 24195787 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.35 0.35 0 46 1 0.34 0.12 78 2 123 "by doubleHit,submitter,freq,cluster" Benign 0.084 6 conservative 608199 19p13.12 peptidoglycan recognition protein 2 1227 rs733743 ZNF306 80317 6 28435350 NM_024493 NP_077819 C/G R3T minus 79697 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 84 0.12 0.13 0.04 224 3 0.16 0.12 260 4 123 "by submitter,freq,cluster" Possibly damaging 1.807 7 Tolerant 0.81 2.95 19 moderately conservative 6p21.33 zinc finger protein 306 1228 rs733743 ZNF306 80317 6 28435350 NM_024493 NP_077819 C/G R3T minus 79697 1303 SEQUENOM CEPH CEPH (92) 92 0.11 0.13 0.04 224 3 0.16 0.12 260 4 123 "by submitter,freq,cluster" Possibly damaging 1.807 7 Tolerant 0.81 2.95 19 moderately conservative 6p21.33 zinc finger protein 306 1229 rs733743 ZNF306 80317 6 28435350 NM_024493 NP_077819 C/G R3T minus 23916317 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.19 0.13 0.04 224 3 0.16 0.12 260 4 123 "by submitter,freq,cluster" Possibly damaging 1.807 7 Tolerant 0.81 2.95 19 moderately conservative 6p21.33 zinc finger protein 306 1230 rs734784 KCNS1 3787 20 43157041 NM_002251 NP_002242 A/G I489V minus 80995 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 80 0.45 0.47 0.02 172 2 0.4 0 84 1 121 "by doubleHit,submitter,freq,cluster" Tolerant 0.38 2.88 41 conservative 602905 20q12 "potassium voltage-gated channel, delayed-rectifier, subfamily S, member 1" 1231 rs734784 KCNS1 3787 20 43157041 NM_002251 NP_002242 A/G I489V minus 12587043 1303 SEQUENOM CEPH CEPH (92) 92 0.48 0.47 0.02 172 2 0.4 0 84 1 121 "by doubleHit,submitter,freq,cluster" Tolerant 0.38 2.88 41 conservative 602905 20q12 "potassium voltage-gated channel, delayed-rectifier, subfamily S, member 1" 1232 rs738792 MMP11 4320 22 22445932 NM_005940 NP_005931 C/T A38V plus 86318 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.05 0.05 0 164 2 0.34 0.02 1563 3 123 "HapMap,doubleHit,freq,cluster" moderately conservative 185261 22q11.23 matrix metalloproteinase 11 (stromelysin 3) 1233 rs738792 MMP11 4320 22 22445932 NM_005940 NP_005931 C/T A38V plus 23607471 1371 PERLEGEN AFD_EUR_PANEL European American (24) 44 0.05 0.05 0 164 2 0.34 0.02 1563 3 123 "HapMap,doubleHit,freq,cluster" moderately conservative 185261 22q11.23 matrix metalloproteinase 11 (stromelysin 3) 1234 rs742493 UNC5CL 222643 6 41106145 NM_173561 NP_775832 A/G R432G minus 91336 1303 SEQUENOM CEPH CEPH (92) 92 0.27 0.24 0.06 132 2 0.06 0.01 1386 3 123 "by cluster,freq" moderately radical 6p21.1 unc-5 homolog C (C. elegans)-like 1235 rs742493 UNC5CL 222643 6 41106145 NM_173561 NP_775832 A/G R432G minus 24435638 1371 PERLEGEN AFD_EUR_PANEL European American (24) 40 0.18 0.24 0.06 132 2 0.06 0.01 1386 3 123 "by cluster,freq" moderately radical 6p21.1 unc-5 homolog C (C. elegans)-like 1236 rs743616 ARSA 410 22 49354183 NM_000487 NP_000478 C/G T391S plus 92782 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.43 0.44 0.02 430 4 0.26 0.03 92 2 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.948 7 Tolerant 0.96 2.75 21 moderately conservative 607574 22q13.33 arylsulfatase A 1237 rs743616 ARSA 410 22 49354183 NM_000487 NP_000478 C/G T391S plus 92782 1303 SEQUENOM CEPH CEPH (92) 92 0.47 0.44 0.02 430 4 0.26 0.03 92 2 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.948 7 Tolerant 0.96 2.75 21 moderately conservative 607574 22q13.33 arylsulfatase A 1238 rs743616 ARSA 410 22 49354183 NM_000487 NP_000478 C/G T391S plus 8485032 693 EGP_SNPS PDR90 NIHPDR 170 0.44 0.44 0.02 430 4 0.26 0.03 92 2 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.948 7 Tolerant 0.96 2.75 21 moderately conservative 607574 22q13.33 arylsulfatase A 1239 rs743616 ARSA 410 22 49354183 NM_000487 NP_000478 C/G T391S plus 24706948 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.44 0.44 0.02 430 4 0.26 0.03 92 2 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.948 7 Tolerant 0.96 2.75 21 moderately conservative 607574 22q13.33 arylsulfatase A 1240 rs751141 EPHX2 2053 8 27429782 NM_001979 NP_001970 C/T R287Q minus 103248 1303 SEQUENOM CEPH CEPH (92) 92 0.14 0.14 0.01 140 2 0.11 0.12 90 2 123 "by doubleHit,submitter,freq,cluster" Possibly damaging 1.595 9 Intolerant 0.02 2.71 84 conservative 132811 8p21-p12 "epoxide hydrolase 2, cytoplasmic" 1241 rs751141 EPHX2 2053 8 27429782 NM_001979 NP_001970 C/T R287Q minus 24085004 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.14 0.01 140 2 0.11 0.12 90 2 123 "by doubleHit,submitter,freq,cluster" Possibly damaging 1.595 9 Intolerant 0.02 2.71 84 conservative 132811 8p21-p12 "epoxide hydrolase 2, cytoplasmic" 1242 rs757110 ABCC8 6833 11 17375053 NM_000352 NP_000343 G/T A1369S minus 128868 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 78 0.32 0.37 0.04 1209 5 0.11 0.16 118 3 123 "by doubleHit,freq,cluster" Benign 0.151 18 moderately conservative 600509 11p15.1 "ATP-binding cassette, sub-family C (CFTR/MRP), member 8" 1243 rs757110 ABCC8 6833 11 17375053 NM_000352 NP_000343 G/T A1369S minus 128868 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 24 0.46 0.37 0.04 1209 5 0.11 0.16 118 3 123 "by doubleHit,freq,cluster" Benign 0.151 18 moderately conservative 600509 11p15.1 "ATP-binding cassette, sub-family C (CFTR/MRP), member 8" 1244 rs757110 ABCC8 6833 11 17375053 NM_000352 NP_000343 G/T A1369S minus 128868 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 94 0.46 0.37 0.04 1209 5 0.11 0.16 118 3 123 "by doubleHit,freq,cluster" Benign 0.151 18 moderately conservative 600509 11p15.1 "ATP-binding cassette, sub-family C (CFTR/MRP), member 8" 1245 rs757110 ABCC8 6833 11 17375053 NM_000352 NP_000343 G/T A1369S minus 128868 1303 SEQUENOM CEPH CEPH (92) 92 0.31 0.37 0.04 1209 5 0.11 0.16 118 3 123 "by doubleHit,freq,cluster" Benign 0.151 18 moderately conservative 600509 11p15.1 "ATP-binding cassette, sub-family C (CFTR/MRP), member 8" 1246 rs757110 ABCC8 6833 11 17375053 NM_000352 NP_000343 G/T A1369S minus 12587336 928 IBARROSO ELY UK (Ely region of East Anglia) 921 0.37 0.37 0.04 1209 5 0.11 0.16 118 3 123 "by doubleHit,freq,cluster" Benign 0.151 18 moderately conservative 600509 11p15.1 "ATP-binding cassette, sub-family C (CFTR/MRP), member 8" 1247 rs757660 SEC14L2 23541 22 29117691 NM_012429 NP_036561 A/G R11K plus 129607 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 80 0.19 0.25 0.04 336 4 0.37 0.1 230 4 123 "HapMap,doubleHit,freq,cluster" Benign 0.308 17 Tolerant 1 2.94 29 conservative 607558 22q12.2 SEC14-like 2 (S. cerevisiae) 1248 rs757660 SEC14L2 23541 22 29117691 NM_012429 NP_036561 A/G R11K plus 5184931 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.28 0.25 0.04 336 4 0.37 0.1 230 4 123 "HapMap,doubleHit,freq,cluster" Benign 0.308 17 Tolerant 1 2.94 29 conservative 607558 22q12.2 SEC14-like 2 (S. cerevisiae) 1249 rs757660 SEC14L2 23541 22 29117691 NM_012429 NP_036561 A/G R11K plus 5184931 1303 SEQUENOM CEPH CEPH (92) 92 0.26 0.25 0.04 336 4 0.37 0.1 230 4 123 "HapMap,doubleHit,freq,cluster" Benign 0.308 17 Tolerant 1 2.94 29 conservative 607558 22q12.2 SEC14-like 2 (S. cerevisiae) 1250 rs757660 SEC14L2 23541 22 29117691 NM_012429 NP_036561 A/G R11K plus 23665295 1371 PERLEGEN AFD_EUR_PANEL European American (24) 44 0.27 0.25 0.04 336 4 0.37 0.1 230 4 123 "HapMap,doubleHit,freq,cluster" Benign 0.308 17 Tolerant 1 2.94 29 conservative 607558 22q12.2 SEC14-like 2 (S. cerevisiae) 1251 rs760357 TPSG1 25823 16 1213491 NM_012467 NP_036599 A/G V60M minus 133243 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.14 0.27 0.07 106 2 0.14 0.02 1506 2 100 "by cluster,freq" conservative 16p13.3 tryptase gamma 1 1252 rs760357 TPSG1 25823 16 1213491 NM_012467 NP_036599 A/G V60M minus 133243 1303 SEQUENOM CEPH CEPH (92) 92 0.29 0.27 0.07 106 2 0.14 0.02 1506 2 100 "by cluster,freq" conservative 16p13.3 tryptase gamma 1 1253 rs760749 MOV10L1 54456 22 48858143 NM_018995 NP_061868 A/C I454L plus 24214763 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.1 0 48 1 0.12 0.11 94 2 123 "by doubleHit,submitter,freq,cluster" conservative 605794 22q13.33 "Mov10l1, Moloney leukemia virus 10-like 1, homolog (mouse)" 1254 rs763361 CD226 10666 18 65682622 NM_006566 NP_006557 C/T S307G plus 149473 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.48 0.45 0.04 236 3 0.34 0.01 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 605397 18q22.3 CD226 antigen 1255 rs763361 CD226 10666 18 65682622 NM_006566 NP_006557 C/T S307G plus 149473 1303 SEQUENOM CEPH CEPH (92) 92 0.41 0.45 0.04 236 3 0.34 0.01 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 605397 18q22.3 CD226 antigen 1256 rs763361 CD226 10666 18 65682622 NM_006566 NP_006557 C/T S307G plus 24509880 1371 PERLEGEN AFD_EUR_PANEL European American (24) 24 0.5 0.45 0.04 236 3 0.34 0.01 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 605397 18q22.3 CD226 antigen 1257 rs764264 VNN3 55350 6 133097427 NM_078625 NP_523239 C/T H33R plus 150727 1303 SEQUENOM CEPH CEPH (92) 92 0.02 0.02 0 92 1 86 by freq conservative 606592 6q23-q24 vanin 3 1258 rs764535 TLR5 7100 1 2901488 NM_003268 NP_003259 A/G T82I plus 151118 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 82 0.04 0.05 0.01 118 2 0.15 0 34 1 86 "by submitter,freq" Tolerant 0.46 2.82 10 moderately conservative 603031 1q41-q42 toll-like receptor 5 1259 rs764535 TLR5 7100 1 2901488 NM_003268 NP_003259 A/G T82I plus 151118 904 AFFY CEPH 36 0.06 0.05 0.01 118 2 0.15 0 34 1 86 "by submitter,freq" Tolerant 0.46 2.82 10 moderately conservative 603031 1q41-q42 toll-like receptor 5 1260 rs765746 ZNF30 90075 19 40126909 NM_194325 NP_919306 C/T Y319C minus 152765 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 84 0.14 0.12 0.02 228 4 0.32 0.04 768 2 119 "by doubleHit,freq,cluster" Possibly damaging 1.608 242 Intolerant 0 2.74 95 radical 19q13.13 zinc finger protein 30 (KOX 28) 1261 rs765746 ZNF30 90075 19 40126909 NM_194325 NP_919306 C/T Y319C minus 152765 902 AFFY Caucasian 26 0.12 0.12 0.02 228 4 0.32 0.04 768 2 119 "by doubleHit,freq,cluster" Possibly damaging 1.608 242 Intolerant 0 2.74 95 radical 19q13.13 zinc finger protein 30 (KOX 28) 1262 rs765746 ZNF30 90075 19 40126909 NM_194325 NP_919306 C/T Y319C minus 152765 904 AFFY CEPH 26 0.15 0.12 0.02 228 4 0.32 0.04 768 2 119 "by doubleHit,freq,cluster" Possibly damaging 1.608 242 Intolerant 0 2.74 95 radical 19q13.13 zinc finger protein 30 (KOX 28) 1263 rs765746 ZNF30 90075 19 40126909 NM_194325 NP_919306 C/T Y319C minus 152765 1303 SEQUENOM CEPH CEPH (92) 92 0.1 0.12 0.02 228 4 0.32 0.04 768 2 119 "by doubleHit,freq,cluster" Possibly damaging 1.608 242 Intolerant 0 2.74 95 radical 19q13.13 zinc finger protein 30 (KOX 28) 1264 rs766173 BRCA2 675 13 31804480 NM_000059 NP_000050 G/T N289H minus 5586314 775 SNP500CANCER CAUC1 Caucasian (31) 60 0.03 0.03 0.01 330 3 0.04 0.03 318 4 120 "by cluster,freq" Possibly damaging 1.699 9 moderately conservative 600185 13q12.3 "breast cancer 2, early onset" 1265 rs766173 BRCA2 675 13 31804480 NM_000059 NP_000050 G/T N289H minus 5586314 1303 SEQUENOM CEPH CEPH (92) 92 0.02 0.03 0.01 330 3 0.04 0.03 318 4 120 "by cluster,freq" Possibly damaging 1.699 9 moderately conservative 600185 13q12.3 "breast cancer 2, early onset" 1266 rs766173 BRCA2 675 13 31804480 NM_000059 NP_000050 G/T N289H minus 16355779 693 EGP_SNPS PDR90 NIHPDR 178 0.04 0.03 0.01 330 3 0.04 0.03 318 4 120 "by cluster,freq" Possibly damaging 1.699 9 moderately conservative 600185 13q12.3 "breast cancer 2, early onset" 1267 rs769193 MPG 4350 16 75652 NM_002434 NP_002425 C/T A258V plus 4388616 693 EGP_SNPS PDR90 NIHPDR 180 0.01 0.01 0 180 1 106 "by cluster,freq" Benign 0.079 10 Tolerant 0.36 2.73 79 moderately conservative 156565 16p13.3 N-methylpurine-DNA glycosylase 1268 rs769242 CCNA2 890 4 123099822 NM_001237 NP_001228 A/G I163V minus 869797 555 UUGC NIH90 NIHPDR 178 0.03 0.03 0.01 410 3 0.02 0.01 298 3 121 "by cluster,freq" Benign 0.106 18 conservative 123835 4q25-q31 cyclin A2 1269 rs769242 CCNA2 890 4 123099822 NM_001237 NP_001228 A/G I163V minus 4478779 693 EGP_SNPS PDR90 NIHPDR 170 0.04 0.03 0.01 410 3 0.02 0.01 298 3 121 "by cluster,freq" Benign 0.106 18 conservative 123835 4q25-q31 cyclin A2 1270 rs769242 CCNA2 890 4 123099822 NM_001237 NP_001228 A/G I163V minus 5586326 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.02 0.03 0.01 410 3 0.02 0.01 298 3 121 "by cluster,freq" Benign 0.106 18 conservative 123835 4q25-q31 cyclin A2 1271 rs769403 GAD1 2571 2 171539042 NM_000817 NP_000808 G/T V474G plus 870094 506 NCBI NIHPDR NIHPDR 86 0.03 0.03 0 86 1 101 "by cluster,freq" Possibly damaging 1.805 21 Tolerant 0.37 2.8 50 moderately radical 605363 2q31 "glutamate decarboxylase 1 (brain, 67kDa)" 1272 rs769416 NBS1 4683 8 91052633 NM_002485 NP_002476 G/T Q216K plus 870110 506 NCBI NIHPDR NIHPDR 156 0.01 0.01 0 332 2 121 "by cluster,freq" Borderline 1.152 8 Tolerant 1 3.08 20 moderately conservative 602667 8q21 Nijmegen breakage syndrome 1 (nibrin) 1273 rs769416 NBS1 4683 8 91052633 NM_002485 NP_002476 G/T Q216K plus 22970238 693 EGP_SNPS PDR90 NIHPDR 176 0.01 0.01 0 332 2 121 "by cluster,freq" Borderline 1.152 8 Tolerant 1 3.08 20 moderately conservative 602667 8q21 Nijmegen breakage syndrome 1 (nibrin) 1274 rs769420 NBS1 4683 8 91051867 NM_002485 NP_002476 A/G P266L plus 870114 506 NCBI NIHPDR NIHPDR 170 0.03 0.02 0.01 346 2 121 "HapMap,freq,cluster" Probably damaging 2.55 8 Intolerant 0.01 3.24 16 moderately conservative 602667 8q21 Nijmegen breakage syndrome 1 (nibrin) 1275 rs769420 NBS1 4683 8 91051867 NM_002485 NP_002476 A/G P266L plus 22970244 693 EGP_SNPS PDR90 NIHPDR 176 0.02 0.02 0.01 346 2 121 "HapMap,freq,cluster" Probably damaging 2.55 8 Intolerant 0.01 3.24 16 moderately conservative 602667 8q21 Nijmegen breakage syndrome 1 (nibrin) 1276 rs769443 FAU 2197 11 64644854 NM_001997 NP_001988 A/G V93M minus 870145 555 UUGC NIH90 NIHPDR 180 0.01 0.01 0 358 2 119 "by cluster,freq" Potentially damaging 1.438 13 Intolerant 0 3.02 74 conservative 134690 11q13 Finkel-Biskis-Reilly murine sarcoma virus (FBR-MuSV) ubiquitously expressed (fox derived); ribosomal protein S30 1277 rs769443 FAU 2197 11 64644854 NM_001997 NP_001988 A/G V93M minus 12709619 693 EGP_SNPS PDR90 NIHPDR 178 0.01 0.01 0 358 2 119 "by cluster,freq" Potentially damaging 1.438 13 Intolerant 0 3.02 74 conservative 134690 11q13 Finkel-Biskis-Reilly murine sarcoma virus (FBR-MuSV) ubiquitously expressed (fox derived); ribosomal protein S30 1278 rs769452 APOE 348 19 50102950 NM_000041 NP_000032 C/T L46P plus 870160 563 DEBNICK MDECODE-1 European-Americans 48 0.02 0.02 0 48 1 86 by freq Potentially damaging 1.381 27 Tolerant 0.26 2.86 26 moderately conservative 107741 19q13.2 apolipoprotein E 1279 rs770087 DUSP6 1848 12 88247241 NM_001946 NP_001937 G/T S144A minus 1798733 1303 SEQUENOM CEPH CEPH (92) 92 0.2 0.2 0.01 140 2 0.05 0.1 964 2 123 "by doubleHit,freq,cluster" Benign 0.134 18 Potentially intolerant 0.1 2.83 45 moderately conservative 602748 12q22-q23 dual specificity phosphatase 6 1280 rs770087 DUSP6 1848 12 88247241 NM_001946 NP_001937 G/T S144A minus 23458622 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.2 0.01 140 2 0.05 0.1 964 2 123 "by doubleHit,freq,cluster" Benign 0.134 18 Potentially intolerant 0.1 2.83 45 moderately conservative 602748 12q22-q23 dual specificity phosphatase 6 1281 rs773123 ERBB3 2065 12 54781265 NM_001982 NP_001973 A/T S1119C minus 1984870 1303 SEQUENOM CEPH CEPH (92) 92 0.47 0.47 0 92 1 121 "by doubleHit,freq,cluster" moderately radical 190151 12q13 v-erb-b2 erythroblastic leukemia viral oncogene homolog 3 (avian) 1282 rs774027 TIMELESS 8914 12 55108645 NM_003920 NP_003911 A/T I455L plus 1986181 1303 SEQUENOM CEPH CEPH (92) 92 0.28 0.3 0.03 140 2 0.25 0.04 94 2 123 "by doubleHit,freq" Benign 0.165 6 conservative 603887 12q12-q13 timeless homolog (Drosophila) 1283 rs774027 TIMELESS 8914 12 55108645 NM_003920 NP_003911 A/T I455L plus 24456217 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.33 0.3 0.03 140 2 0.25 0.04 94 2 123 "by doubleHit,freq" Benign 0.165 6 conservative 603887 12q12-q13 timeless homolog (Drosophila) 1284 rs774047 TIMELESS 8914 12 55102189 NM_003920 NP_003911 C/T R831Q plus 1986172 1303 SEQUENOM CEPH CEPH (92) 92 0.48 0.43 0.1 140 2 0.38 0.04 1572 3 123 "by doubleHit,freq,cluster" Benign 0.084 6 conservative 603887 12q12-q13 timeless homolog (Drosophila) 1285 rs774047 TIMELESS 8914 12 55102189 NM_003920 NP_003911 C/T R831Q plus 24456190 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.33 0.43 0.1 140 2 0.38 0.04 1572 3 123 "by doubleHit,freq,cluster" Benign 0.084 6 conservative 603887 12q12-q13 timeless homolog (Drosophila) 1286 rs782572 PNPT1 87178 2 55823771 NM_033109 NP_149100 C/T I121V plus 3635716 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.48 0.48 0 120 1 123 "HapMap,doubleHit,submitter,freq" Benign 0.148 9 conservative 2p15 polyribonucleotide nucleotidyltransferase 1 1287 rs783396 AIM1 202 6 107094063 XM_166300 XP_166300 A/C E1819A plus 1615915 1303 SEQUENOM CEPH CEPH (92) 92 0.2 0.18 0.03 140 2 0.08 0.01 94 2 123 "by submitter,freq,cluster" moderately radical 601797 6q21 absent in melanoma 1 1288 rs783396 AIM1 202 6 107094063 XM_166300 XP_166300 A/C E1819A plus 24360909 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.18 0.03 140 2 0.08 0.01 94 2 123 "by submitter,freq,cluster" moderately radical 601797 6q21 absent in melanoma 1 1289 rs783420 AIM1 202 6 107066629 XM_166300 XP_166300 C/G G530A minus 2281838 1303 SEQUENOM CEPH CEPH (92) 92 0.44 0.44 0 92 1 120 "by doubleHit,freq" moderately conservative 601797 6q21 absent in melanoma 1 1290 rs783423 AIM1 202 6 107065437 XM_166300 XP_166300 A/G S311N plus 23324559 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.04 0 48 1 0.2 0.18 94 2 123 "by doubleHit,freq,cluster" conservative 601797 6q21 absent in melanoma 1 1291 rs785467 PIK3R3 8503 1 46233579 NM_003629 NP_003620 A/T N283K minus 1927292 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.36 0.36 0.07 318 4 0.31 0.01 1570 3 123 "HapMap,doubleHit,freq,cluster" Potentially damaging 1.26 37 Tolerant 1 3.04 35 moderately conservative 606076 1p34.1 "phosphoinositide-3-kinase, regulatory subunit, polypeptide 3 (p55, gamma)" 1292 rs785467 PIK3R3 8503 1 46233579 NM_003629 NP_003620 A/T N283K minus 1927292 1303 SEQUENOM CEPH CEPH (92) 92 0.42 0.36 0.07 318 4 0.31 0.01 1570 3 123 "HapMap,doubleHit,freq,cluster" Potentially damaging 1.26 37 Tolerant 1 3.04 35 moderately conservative 606076 1p34.1 "phosphoinositide-3-kinase, regulatory subunit, polypeptide 3 (p55, gamma)" 1293 rs785467 PIK3R3 8503 1 46233579 NM_003629 NP_003620 A/T N283K minus 3177818 619 WICVAR MITOGPOP6 CORIELL Mixed 58 0.24 0.36 0.07 318 4 0.31 0.01 1570 3 123 "HapMap,doubleHit,freq,cluster" Potentially damaging 1.26 37 Tolerant 1 3.04 35 moderately conservative 606076 1p34.1 "phosphoinositide-3-kinase, regulatory subunit, polypeptide 3 (p55, gamma)" 1294 rs785467 PIK3R3 8503 1 46233579 NM_003629 NP_003620 A/T N283K minus 24243577 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.42 0.36 0.07 318 4 0.31 0.01 1570 3 123 "HapMap,doubleHit,freq,cluster" Potentially damaging 1.26 37 Tolerant 1 3.04 35 moderately conservative 606076 1p34.1 "phosphoinositide-3-kinase, regulatory subunit, polypeptide 3 (p55, gamma)" 1295 rs788908 ADAMTS3 9508 4 73779321 NM_014243 NP_055058 A/G R138K minus 2198837 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.41 0.26 0.19 248 4 0.26 0.03 1568 4 120 "HapMap,doubleHit,submitter,freq,cluster" Borderline 1.189 8 conservative 605011 4q21.1 "a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 3" 1296 rs788908 ADAMTS3 9508 4 73779321 NM_014243 NP_055058 A/G R138K minus 2198837 902 AFFY Caucasian 24 0.33 0.26 0.19 248 4 0.26 0.03 1568 4 120 "HapMap,doubleHit,submitter,freq,cluster" Borderline 1.189 8 conservative 605011 4q21.1 "a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 3" 1297 rs788908 ADAMTS3 9508 4 73779321 NM_014243 NP_055058 A/G R138K minus 2198837 904 AFFY CEPH 12 0.25 0.26 0.19 248 4 0.26 0.03 1568 4 120 "HapMap,doubleHit,submitter,freq,cluster" Borderline 1.189 8 conservative 605011 4q21.1 "a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 3" 1298 rs788908 ADAMTS3 9508 4 73779321 NM_014243 NP_055058 A/G R138K minus 2198837 1303 SEQUENOM CEPH CEPH (92) 92 0.05 0.26 0.19 248 4 0.26 0.03 1568 4 120 "HapMap,doubleHit,submitter,freq,cluster" Borderline 1.189 8 conservative 605011 4q21.1 "a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 3" 1299 rs794001 N4BP2 55728 4 39944128 NM_018177 NP_060647 A/G D611N plus 2193078 760 TSC-CSHL CEL_CAUCASIAN CELERA Caucasians (30) 60 0.28 0.26 0.04 108 2 0.18 0.09 166 3 123 "by doubleHit,submitter,freq,cluster" conservative 4p14 Nedd4 binding protein 2 1300 rs794001 N4BP2 55728 4 39944128 NM_018177 NP_060647 A/G D611N plus 23719790 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.23 0.26 0.04 108 2 0.18 0.09 166 3 123 "by doubleHit,submitter,freq,cluster" conservative 4p14 Nedd4 binding protein 2 1301 rs801720 CERK 64781 22 45402678 NM_182661 NP_872602 G/T E113D minus 8305886 1303 SEQUENOM CEPH CEPH (92) 92 0.39 0.39 0 92 1 0.38 0 1492 1 120 "by doubleHit,freq,cluster" conservative 22q13.31 ceramide kinase 1302 rs805657 SLK 9748 10 105752581 NM_014720 NP_055535 A/G C552Y plus 1951606 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.18 0.17 0.02 260 3 0.19 0.22 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Probably damaging 2.6 10 radical 10q25.1 SNF1 sucrose nonfermenting like kinase (yeast) 1303 rs805657 SLK 9748 10 105752581 NM_014720 NP_055535 A/G C552Y plus 1951606 1303 SEQUENOM CEPH CEPH (92) 92 0.15 0.17 0.02 260 3 0.19 0.22 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Probably damaging 2.6 10 radical 10q25.1 SNF1 sucrose nonfermenting like kinase (yeast) 1304 rs805657 SLK 9748 10 105752581 NM_014720 NP_055535 A/G C552Y plus 23510988 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.19 0.17 0.02 260 3 0.19 0.22 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Probably damaging 2.6 10 radical 10q25.1 SNF1 sucrose nonfermenting like kinase (yeast) 1305 rs814628 LIPF 8513 10 90419632 NM_004190 NP_004181 A/G T161A plus 1764627 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.14 0.15 0.01 260 3 0.3 0.05 1392 3 123 "HapMap,doubleHit,submitter,freq,cluster" Possibly damaging 1.802 44 Intolerant 0.01 2.79 39 moderately conservative 601980 10q23.31 "lipase, gastric" 1306 rs814628 LIPF 8513 10 90419632 NM_004190 NP_004181 A/G T161A plus 1764627 1303 SEQUENOM CEPH CEPH (92) 92 0.15 0.15 0.01 260 3 0.3 0.05 1392 3 123 "HapMap,doubleHit,submitter,freq,cluster" Possibly damaging 1.802 44 Intolerant 0.01 2.79 39 moderately conservative 601980 10q23.31 "lipase, gastric" 1307 rs814628 LIPF 8513 10 90419632 NM_004190 NP_004181 A/G T161A plus 24081117 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.17 0.15 0.01 260 3 0.3 0.05 1392 3 123 "HapMap,doubleHit,submitter,freq,cluster" Possibly damaging 1.802 44 Intolerant 0.01 2.79 39 moderately conservative 601980 10q23.31 "lipase, gastric" 1308 rs820196 RECQL5 9400 17 71139134 NM_004259 NP_004250 C/T D480G plus 1802369 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.22 0.21 0.02 168 2 0.26 0.08 94 2 123 "HapMap,doubleHit,freq,cluster" Benign 0.103 7 moderately conservative 603781 17q25.2-q25.3 RecQ protein-like 5 1309 rs820196 RECQL5 9400 17 71139134 NM_004259 NP_004250 C/T D480G plus 24098205 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.19 0.21 0.02 168 2 0.26 0.08 94 2 123 "HapMap,doubleHit,freq,cluster" Benign 0.103 7 moderately conservative 603781 17q25.2-q25.3 RecQ protein-like 5 1310 rs827528 FZD6 8323 8 104381608 NM_003506 NP_003497 A/G M33V plus 1989018 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.3 0.26 0.06 212 2 119 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 0.25 2.79 85 conservative 603409 8q22.3-q23.1 frizzled homolog 6 (Drosophila) 1311 rs827528 FZD6 8323 8 104381608 NM_003506 NP_003497 A/G M33V plus 1989018 1303 SEQUENOM CEPH CEPH (92) 92 0.21 0.26 0.06 212 2 119 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 0.25 2.79 85 conservative 603409 8q22.3-q23.1 frizzled homolog 6 (Drosophila) 1312 rs832582 MAP3K1 4214 5 56213500 XM_042066 XP_042066 A/G V1040I plus 1317910 1303 SEQUENOM CEPH CEPH (92) 92 0.15 0.16 0.01 140 2 0.35 0.07 94 2 123 "by submitter,freq,cluster" conservative 600982 5q11.2 mitogen-activated protein kinase kinase kinase 1 1313 rs832582 MAP3K1 4214 5 56213500 XM_042066 XP_042066 A/G V1040I plus 23955529 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.17 0.16 0.01 140 2 0.35 0.07 94 2 123 "by submitter,freq,cluster" conservative 600982 5q11.2 mitogen-activated protein kinase kinase kinase 1 1314 rs838827 IKBKAP 8518 9 108748207 NM_003640 NP_003631 C/T R525Q plus 1666273 1303 SEQUENOM CEPH CEPH (92) 92 0.03 0.03 0.01 140 2 120 by doubleHit Benign 0.387 9 Tolerant 0.54 2.94 13 conservative 603722 9q31 "inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase complex-associated protein" 1315 rs838827 IKBKAP 8518 9 108748207 NM_003640 NP_003631 C/T R525Q plus 3177966 619 WICVAR MITOGPOP6 CORIELL Mixed 48 0.02 0.03 0.01 140 2 120 by doubleHit Benign 0.387 9 Tolerant 0.54 2.94 13 conservative 603722 9q31 "inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase complex-associated protein" 1316 rs843358 EIF2B5 8893 3 185343945 NM_003907 NP_003898 C/T I587V minus 2545226 1303 SEQUENOM CEPH CEPH (92) 92 0.26 0.26 0 92 1 0.45 0 1494 1 121 "by doubleHit,freq,cluster" Benign 0.3 6 conservative 603945 3q27.3 "eukaryotic translation initiation factor 2B, subunit 5 epsilon, 82kDa" 1317 rs846266 GLI3 2737 7 41861462 NM_000168 NP_000159 A/G T183A minus 1403663 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 84 0.45 0.46 0.04 404 4 0.31 0.17 314 5 123 "by doubleHit,freq,cluster" Benign 0.039 5 moderately conservative 165240 7p13 GLI-Kruppel family member GLI3 (Greig cephalopolysyndactyly syndrome) 1318 rs846266 GLI3 2737 7 41861462 NM_000168 NP_000159 A/G T183A minus 1403663 1303 SEQUENOM CEPH CEPH (92) 92 0.45 0.46 0.04 404 4 0.31 0.17 314 5 123 "by doubleHit,freq,cluster" Benign 0.039 5 moderately conservative 165240 7p13 GLI-Kruppel family member GLI3 (Greig cephalopolysyndactyly syndrome) 1319 rs846266 GLI3 2737 7 41861462 NM_000168 NP_000159 A/G T183A minus 24195653 1371 PERLEGEN AFD_EUR_PANEL European American (24) 44 0.39 0.46 0.04 404 4 0.31 0.17 314 5 123 "by doubleHit,freq,cluster" Benign 0.039 5 moderately conservative 165240 7p13 GLI-Kruppel family member GLI3 (Greig cephalopolysyndactyly syndrome) 1320 rs846266 GLI3 2737 7 41861462 NM_000168 NP_000159 A/G T183A minus 24810597 1303 SEQUENOM CEPH CEPH (92) 184 0.49 0.46 0.04 404 4 0.31 0.17 314 5 123 "by doubleHit,freq,cluster" Benign 0.039 5 moderately conservative 165240 7p13 GLI-Kruppel family member GLI3 (Greig cephalopolysyndactyly syndrome) 1321 rs853678 ZNF323 64288 6 28405292 NM_145909 NP_665916 A/T T50S minus 17877537 1303 SEQUENOM CEPH CEPH (92) 92 0.18 0.16 0.05 136 2 0.18 0.03 1556 3 123 "by doubleHit,submitter,freq,cluster" Tolerant 0.21 2.78 28 moderately conservative 6p21.31 zinc finger protein 323 1322 rs853678 ZNF323 64288 6 28405292 NM_145909 NP_665916 A/T T50S minus 23290944 1371 PERLEGEN AFD_EUR_PANEL European American (24) 44 0.11 0.16 0.05 136 2 0.18 0.03 1556 3 123 "by doubleHit,submitter,freq,cluster" Tolerant 0.21 2.78 28 moderately conservative 6p21.31 zinc finger protein 323 1323 rs854524 PPP1R9A 55607 7 94543462 XM_371933 XP_371933 A/G R1017Q plus 1847017 1303 SEQUENOM CEPH CEPH (92) 92 0.47 0.46 0.02 140 2 0.4 0.08 90 2 123 "by doubleHit,submitter,freq,cluster" conservative 602468 7q21.3 "protein phosphatase 1, regulatory (inhibitor) subunit 9A" 1324 rs854524 PPP1R9A 55607 7 94543462 XM_371933 XP_371933 A/G R1017Q plus 24194066 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.44 0.46 0.02 140 2 0.4 0.08 90 2 123 "by doubleHit,submitter,freq,cluster" conservative 602468 7q21.3 "protein phosphatase 1, regulatory (inhibitor) subunit 9A" 1325 rs855314 PGM1 5236 1 63807132 NM_002633 NP_002624 C/T I88V minus 2583793 902 AFFY Caucasian 24 0.08 0.11 0.06 36 2 0.12 0.04 62 3 116 "by doubleHit,submitter,freq,cluster" Benign 0.155 95 Tolerant 1 2.82 108 conservative 171900 1p31 phosphoglucomutase 1 1326 rs855314 PGM1 5236 1 63807132 NM_002633 NP_002624 C/T I88V minus 2583793 904 AFFY CEPH 12 0.17 0.11 0.06 36 2 0.12 0.04 62 3 116 "by doubleHit,submitter,freq,cluster" Benign 0.155 95 Tolerant 1 2.82 108 conservative 171900 1p31 phosphoglucomutase 1 1327 rs855791 TMPRSS6 164656 22 35787436 NM_153609 NP_705837 C/T V736A minus 24601298 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.41 0.41 0 46 1 0.29 0.17 92 2 123 "by doubleHit,submitter,freq,cluster" Tolerant 0.66 2.78 36 moderately conservative 22q13.1 "transmembrane protease, serine 6" 1328 rs859210 AKR7A2 8574 1 19380011 NM_003689 NP_003680 A/G E180K minus 2040466 1303 SEQUENOM CEPH CEPH (92) 92 0.05 0.05 0 92 1 98 by freq Potentially damaging 1.47 27 Intolerant 0.02 2.77 20 moderately conservative 603418 1p35.1-p36.23 "aldo-keto reductase family 7, member A2 (aflatoxin aldehyde reductase)" 1329 rs861539 XRCC3 7517 14 103235506 NM_005432 NP_005423 C/T T241M minus 1719048 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 84 0.35 0.31 0.1 416 4 0.21 0.09 508 6 119 "by cluster,freq" Potentially intolerant 0.07 2.78 11 moderately conservative 600675 14q32.3 X-ray repair complementing defective repair in Chinese hamster cells 3 1330 rs861539 XRCC3 7517 14 103235506 NM_005432 NP_005423 C/T T241M minus 4472483 693 EGP_SNPS PDR90 NIHPDR 180 0.22 0.31 0.1 416 4 0.21 0.09 508 6 119 "by cluster,freq" Potentially intolerant 0.07 2.78 11 moderately conservative 600675 14q32.3 X-ray repair complementing defective repair in Chinese hamster cells 3 1331 rs861539 XRCC3 7517 14 103235506 NM_005432 NP_005423 C/T T241M minus 4472483 1303 SEQUENOM CEPH CEPH (92) 92 0.35 0.31 0.1 416 4 0.21 0.09 508 6 119 "by cluster,freq" Potentially intolerant 0.07 2.78 11 moderately conservative 600675 14q32.3 X-ray repair complementing defective repair in Chinese hamster cells 3 1332 rs861539 XRCC3 7517 14 103235506 NM_005432 NP_005423 C/T T241M minus 5586983 775 SNP500CANCER CAUC1 Caucasian (31) 60 0.45 0.31 0.1 416 4 0.21 0.09 508 6 119 "by cluster,freq" Potentially intolerant 0.07 2.78 11 moderately conservative 600675 14q32.3 X-ray repair complementing defective repair in Chinese hamster cells 3 1333 rs866484 IFI16 3428 1 155799550 NM_005531 NP_005522 C/G S179T minus 1290164 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 12 0.17 0.17 0.03 194 3 0.42 0 48 2 120 "by doubleHit,freq,cluster" Tolerant 1 3.03 31 moderately conservative 147586 1q22 "interferon, gamma-inducible protein 16" 1334 rs866484 IFI16 3428 1 155799550 NM_005531 NP_005522 C/G S179T minus 1290164 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 90 0.2 0.17 0.03 194 3 0.42 0 48 2 120 "by doubleHit,freq,cluster" Tolerant 1 3.03 31 moderately conservative 147586 1q22 "interferon, gamma-inducible protein 16" 1335 rs866484 IFI16 3428 1 155799550 NM_005531 NP_005522 C/G S179T minus 1290164 1303 SEQUENOM CEPH CEPH (92) 92 0.15 0.17 0.03 194 3 0.42 0 48 2 120 "by doubleHit,freq,cluster" Tolerant 1 3.03 31 moderately conservative 147586 1q22 "interferon, gamma-inducible protein 16" 1336 rs867168 ZNF554 115196 19 2784802 NM_152303 NP_689516 C/T E139G minus 1288955 1303 SEQUENOM CEPH CEPH (92) 92 0.29 0.26 0.05 140 2 0.25 0.3 94 2 123 "by doubleHit,freq" Tolerant 0.37 2.79 20 moderately conservative 19p13.3 zinc finger protein 554 1337 rs867168 ZNF554 115196 19 2784802 NM_152303 NP_689516 C/T E139G minus 24190893 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.26 0.05 140 2 0.25 0.3 94 2 123 "by doubleHit,freq" Tolerant 0.37 2.79 20 moderately conservative 19p13.3 zinc finger protein 554 1338 rs867169 ZNF554 115196 19 2784864 NM_152303 NP_689516 C/T V160I minus 1288956 1303 SEQUENOM CEPH CEPH (92) 92 0.2 0.2 0.01 140 2 0.29 0.25 94 2 123 "by doubleHit,submitter,freq" Tolerant 0.39 2.79 20 conservative 19p13.3 zinc finger protein 554 1339 rs867169 ZNF554 115196 19 2784864 NM_152303 NP_689516 C/T V160I minus 24190895 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.2 0.01 140 2 0.29 0.25 94 2 123 "by doubleHit,submitter,freq" Tolerant 0.39 2.79 20 conservative 19p13.3 zinc finger protein 554 1340 rs867186 PROCR 10544 20 33228215 NM_006404 NP_006395 A/G S219G plus 2982093 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 44 0.18 0.13 0.06 184 3 0.06 0.01 140 3 123 "by doubleHit,freq" Benign 0.45 5 moderately conservative 600646 20q11.2 "protein C receptor, endothelial (EPCR)" 1341 rs867186 PROCR 10544 20 33228215 NM_006404 NP_006395 A/G S219G plus 8375245 1303 SEQUENOM CEPH CEPH (92) 92 0.08 0.13 0.06 184 3 0.06 0.01 140 3 123 "by doubleHit,freq" Benign 0.45 5 moderately conservative 600646 20q11.2 "protein C receptor, endothelial (EPCR)" 1342 rs867186 PROCR 10544 20 33228215 NM_006404 NP_006395 A/G S219G plus 24537849 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.17 0.13 0.06 184 3 0.06 0.01 140 3 123 "by doubleHit,freq" Benign 0.45 5 moderately conservative 600646 20q11.2 "protein C receptor, endothelial (EPCR)" 1343 rs867228 FPR1 2357 19 56941023 NM_002029 NP_002020 A/C E346A minus 1289025 885 TSC-CSHL HapMap-CEPH-30-trios 116 0.22 0.27 0.07 256 3 0.26 0.03 810 3 123 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.952 21 Tolerant 0.34 3.06 22 moderately radical 136537 19q13.4 formyl peptide receptor 1 1344 rs867228 FPR1 2357 19 56941023 NM_002029 NP_002020 A/C E346A minus 1289025 1303 SEQUENOM CEPH CEPH (92) 92 0.35 0.27 0.07 256 3 0.26 0.03 810 3 123 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.952 21 Tolerant 0.34 3.06 22 moderately radical 136537 19q13.4 formyl peptide receptor 1 1345 rs867228 FPR1 2357 19 56941023 NM_002029 NP_002020 A/C E346A minus 24198505 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.23 0.27 0.07 256 3 0.26 0.03 810 3 123 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.952 21 Tolerant 0.34 3.06 22 moderately radical 136537 19q13.4 formyl peptide receptor 1 1346 rs869457 LAMC3 10319 9 130954005 NM_006059 NP_006050 A/G P522S minus 1291793 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 82 0.37 0.3 0.09 174 2 0.2 0.01 1572 2 120 "by doubleHit,freq,cluster" Tolerant 0.98 2.83 17 moderately conservative 604349 9q31-q34 "laminin, gamma 3" 1347 rs869457 LAMC3 10319 9 130954005 NM_006059 NP_006050 A/G P522S minus 1291793 1303 SEQUENOM CEPH CEPH (92) 92 0.24 0.3 0.09 174 2 0.2 0.01 1572 2 120 "by doubleHit,freq,cluster" Tolerant 0.98 2.83 17 moderately conservative 604349 9q31-q34 "laminin, gamma 3" 1348 rs871443 ITGB4 3691 17 71265098 NM_000213 NP_000204 C/T L1779P plus 1294606 1303 SEQUENOM CEPH CEPH (92) 92 0.21 0.21 0 92 1 121 "by doubleHit,freq,cluster" Benign 0.377 8 moderately conservative 147557 17q11-qter "integrin, beta 4" 1349 rs871545 ZNF295 49854 21 42286720 NM_020727 NP_065778 A/G N185S minus 1294761 1303 SEQUENOM CEPH CEPH (92) 92 0.16 0.16 0 92 1 111 by freq conservative 21q22.3 zinc finger protein 295 1350 rs871546 ZNF295 49854 21 42286622 NM_020727 NP_065778 A/C K218Q minus 1294762 1303 SEQUENOM CEPH CEPH (92) 92 0.47 0.38 0.17 140 2 0.04 0.04 94 2 123 "by doubleHit,freq,cluster" moderately conservative 21q22.3 zinc finger protein 295 1351 rs871546 ZNF295 49854 21 42286622 NM_020727 NP_065778 A/C K218Q minus 24605064 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.38 0.17 140 2 0.04 0.04 94 2 123 "by doubleHit,freq,cluster" moderately conservative 21q22.3 zinc finger protein 295 1352 rs874808 DNAH8 1769 6 38881271 NM_001371 NP_001362 C/T G807E minus 1299055 902 AFFY Caucasian 22 0.45 0.42 0.05 174 4 0.37 0.13 156 5 123 "by doubleHit,freq,cluster" Potentially damaging 1.414 13 moderately conservative 603337 6p21.31-p21.1 "dynein, axonemal, heavy polypeptide 8" 1353 rs874808 DNAH8 1769 6 38881271 NM_001371 NP_001362 C/T G807E minus 1299055 904 AFFY CEPH 12 0.33 0.42 0.05 174 4 0.37 0.13 156 5 123 "by doubleHit,freq,cluster" Potentially damaging 1.414 13 moderately conservative 603337 6p21.31-p21.1 "dynein, axonemal, heavy polypeptide 8" 1354 rs874808 DNAH8 1769 6 38881271 NM_001371 NP_001362 C/T G807E minus 1299055 1303 SEQUENOM CEPH CEPH (92) 92 0.4 0.42 0.05 174 4 0.37 0.13 156 5 123 "by doubleHit,freq,cluster" Potentially damaging 1.414 13 moderately conservative 603337 6p21.31-p21.1 "dynein, axonemal, heavy polypeptide 8" 1355 rs874808 DNAH8 1769 6 38881271 NM_001371 NP_001362 C/T G807E minus 24370109 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.48 0.42 0.05 174 4 0.37 0.13 156 5 123 "by doubleHit,freq,cluster" Potentially damaging 1.414 13 moderately conservative 603337 6p21.31-p21.1 "dynein, axonemal, heavy polypeptide 8" 1356 rs875379 LAMA5 3911 20 60335381 NM_005560 NP_005551 A/G H1717Y plus 1299815 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.1 0.11 0.02 166 2 0.11 0 46 1 123 "HapMap,freq" Possibly damaging 1.834 6 Tolerant 0.35 2.84 12 moderately conservative 601033 20q13.2-q13.3 "laminin, alpha 5" 1357 rs875379 LAMA5 3911 20 60335381 NM_005560 NP_005551 A/G H1717Y plus 24601596 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.11 0.02 166 2 0.11 0 46 1 123 "HapMap,freq" Possibly damaging 1.834 6 Tolerant 0.35 2.84 12 moderately conservative 601033 20q13.2-q13.3 "laminin, alpha 5" 1358 rs878756 MKL1 57591 22 39139000 NM_020831 NP_065882 A/G S648G minus 7998468 1303 SEQUENOM CEPH CEPH (92) 92 0.46 0.4 0.11 140 2 0.2 0.11 94 2 123 "by doubleHit,freq,cluster" Potentially intolerant 0.07 2.83 20 moderately conservative 606078 22q13 megakaryoblastic leukemia (translocation) 1 1359 rs878756 MKL1 57591 22 39139000 NM_020831 NP_065882 A/G S648G minus 24539613 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.29 0.4 0.11 140 2 0.2 0.11 94 2 123 "by doubleHit,freq,cluster" Potentially intolerant 0.07 2.83 20 moderately conservative 606078 22q13 megakaryoblastic leukemia (translocation) 1 1360 rs880303 GJA10 81025 1 39009375 NM_030772 NP_110399 C/T V497I plus 1306346 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.49 0.46 0.05 294 5 0.32 0.11 162 5 123 "HapMap,doubleHit,submitter,freq" conservative 1p34 "gap junction protein, alpha 10, 59kDa" 1361 rs880303 GJA10 81025 1 39009375 NM_030772 NP_110399 C/T V497I plus 1306346 902 AFFY Caucasian 24 0.42 0.46 0.05 294 5 0.32 0.11 162 5 123 "HapMap,doubleHit,submitter,freq" conservative 1p34 "gap junction protein, alpha 10, 59kDa" 1362 rs880303 GJA10 81025 1 39009375 NM_030772 NP_110399 C/T V497I plus 1306346 904 AFFY CEPH 10 0.3 0.46 0.05 294 5 0.32 0.11 162 5 123 "HapMap,doubleHit,submitter,freq" conservative 1p34 "gap junction protein, alpha 10, 59kDa" 1363 rs880303 GJA10 81025 1 39009375 NM_030772 NP_110399 C/T V497I plus 1306346 1303 SEQUENOM CEPH CEPH (92) 92 0.43 0.46 0.05 294 5 0.32 0.11 162 5 123 "HapMap,doubleHit,submitter,freq" conservative 1p34 "gap junction protein, alpha 10, 59kDa" 1364 rs880303 GJA10 81025 1 39009375 NM_030772 NP_110399 C/T V497I plus 24260345 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.48 0.46 0.05 294 5 0.32 0.11 162 5 123 "HapMap,doubleHit,submitter,freq" conservative 1p34 "gap junction protein, alpha 10, 59kDa" 1365 rs880633 CHI3L1 1116 1 199884458 NM_001276 NP_001267 C/T R145G plus 1306850 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.43 0.42 0.08 248 4 0.36 0.03 1576 3 123 "by doubleHit,freq,cluster" Probably damaging 2.271 34 Intolerant 0 2.75 66 moderately radical 601525 1q32.1 chitinase 3-like 1 (cartilage glycoprotein-39) 1366 rs880633 CHI3L1 1116 1 199884458 NM_001276 NP_001267 C/T R145G plus 1306850 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 94 0.49 0.42 0.08 248 4 0.36 0.03 1576 3 123 "by doubleHit,freq,cluster" Probably damaging 2.271 34 Intolerant 0 2.75 66 moderately radical 601525 1q32.1 chitinase 3-like 1 (cartilage glycoprotein-39) 1367 rs880633 CHI3L1 1116 1 199884458 NM_001276 NP_001267 C/T R145G plus 1306850 1303 SEQUENOM CEPH CEPH (92) 92 0.33 0.42 0.08 248 4 0.36 0.03 1576 3 123 "by doubleHit,freq,cluster" Probably damaging 2.271 34 Intolerant 0 2.75 66 moderately radical 601525 1q32.1 chitinase 3-like 1 (cartilage glycoprotein-39) 1368 rs880633 CHI3L1 1116 1 199884458 NM_001276 NP_001267 C/T R145G plus 24256121 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.44 0.42 0.08 248 4 0.36 0.03 1576 3 123 "by doubleHit,freq,cluster" Probably damaging 2.271 34 Intolerant 0 2.75 66 moderately radical 601525 1q32.1 chitinase 3-like 1 (cartilage glycoprotein-39) 1369 rs882709 KIAA0625 23064 9 132234560 NM_015046 NP_055861 C/G A660G minus 1309695 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.03 0.03 0.01 168 2 0.23 0.17 149 5 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 608465 9q34.3 senataxin 1370 rs882709 KIAA0625 23064 9 132234560 NM_015046 NP_055861 C/G A660G minus 24002655 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.03 0.01 168 2 0.23 0.17 149 5 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 608465 9q34.3 senataxin 1371 rs885479 MC1R 4157 16 88513655 NM_002386 NP_002377 A/G R163Q plus 1313046 1303 SEQUENOM CEPH CEPH (92) 92 0.08 0.06 0.04 138 2 0.02 0 46 1 106 "by doubleHit,freq,cluster" Benign 0.517 210 Tolerant 0.29 2.8 286 conservative 155555 16q24.3 melanocortin 1 receptor (alpha melanocyte stimulating hormone receptor) 1372 rs885479 MC1R 4157 16 88513655 NM_002386 NP_002377 A/G R163Q plus 4472738 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.02 0.06 0.04 138 2 0.02 0 46 1 106 "by doubleHit,freq,cluster" Benign 0.517 210 Tolerant 0.29 2.8 286 conservative 155555 16q24.3 melanocortin 1 receptor (alpha melanocyte stimulating hormone receptor) 1373 rs886016 SARDH 1757 9 133585183 NM_007101 NP_009032 A/G M648V minus 1313716 1303 SEQUENOM CEPH CEPH (92) 92 0.28 0.34 0.12 138 2 0.33 0.15 84 2 123 "by doubleHit,freq,cluster" Tolerant 0.89 2.81 24 conservative 604455 9q33-q34 sarcosine dehydrogenase 1374 rs886016 SARDH 1757 9 133585183 NM_007101 NP_009032 A/G M648V minus 24687247 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.46 0.34 0.12 138 2 0.33 0.15 84 2 123 "by doubleHit,freq,cluster" Tolerant 0.89 2.81 24 conservative 604455 9q33-q34 sarcosine dehydrogenase 1375 rs887241 ALDH3A1 218 17 19586530 NM_000691 NP_000682 G/T S134A minus 1315276 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 6 0.5 0.42 0.06 138 3 0.14 0.1 140 4 123 "by doubleHit,freq,cluster" Benign 0.408 38 Tolerant 0.98 2.79 54 moderately conservative 100660 17p11.2 "aldehyde dehydrogenase 3 family, memberA1" 1376 rs887241 ALDH3A1 218 17 19586530 NM_000691 NP_000682 G/T S134A minus 1315276 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 86 0.45 0.42 0.06 138 3 0.14 0.1 140 4 123 "by doubleHit,freq,cluster" Benign 0.408 38 Tolerant 0.98 2.79 54 moderately conservative 100660 17p11.2 "aldehyde dehydrogenase 3 family, memberA1" 1377 rs887241 ALDH3A1 218 17 19586530 NM_000691 NP_000682 G/T S134A minus 24596928 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.35 0.42 0.06 138 3 0.14 0.1 140 4 123 "by doubleHit,freq,cluster" Benign 0.408 38 Tolerant 0.98 2.79 54 moderately conservative 100660 17p11.2 "aldehyde dehydrogenase 3 family, memberA1" 1378 rs890802 COL23A1 91522 5 177615983 NM_173465 NP_775736 A/G T287A minus 24373538 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.48 0.48 0 48 1 0.43 0.08 94 2 123 "by doubleHit,submitter,freq,cluster" Tolerant 0.61 2.77 14 moderately conservative 5q35.3 "collagen, type XXIII, alpha 1" 1379 rs893253 PIP5K3 200576 2 209016034 NM_015040 NP_055855 C/G T998S minus 1323017 1303 SEQUENOM CEPH CEPH (92) 92 0.02 0.02 0 92 1 121 "by doubleHit,freq,cluster" moderately conservative 2q34 "phosphatidylinositol-3-phosphate/phosphatidylinositol 5-kinase, type III" 1380 rs893254 PIP5K3 200576 2 209016025 NM_015040 NP_055855 A/T Q995L minus 1323018 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 84 0.05 0.05 0 84 1 0.22 0 82 1 121 "by doubleHit,freq,cluster" moderately radical 2q34 "phosphatidylinositol-3-phosphate/phosphatidylinositol 5-kinase, type III" 1381 rs897945 THAP9 79725 4 84195441 NM_024672 NP_078948 A/C L299F minus 1328858 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.46 0.43 0.06 260 3 0.29 0.04 1590 3 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 4q21.3 THAP domain containing 9 1382 rs897945 THAP9 79725 4 84195441 NM_024672 NP_078948 A/C L299F minus 1328858 1303 SEQUENOM CEPH CEPH (92) 92 0.36 0.43 0.06 260 3 0.29 0.04 1590 3 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 4q21.3 THAP domain containing 9 1383 rs897945 THAP9 79725 4 84195441 NM_024672 NP_078948 A/C L299F minus 24236182 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.48 0.43 0.06 260 3 0.29 0.04 1590 3 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 4q21.3 THAP domain containing 9 1384 rs902790 GPR156 165829 3 121369466 NM_153002 NP_694547 A/T E516D minus 23255540 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.05 0.05 94 2 123 "by cluster,freq" conservative 3q13.33 G protein-coupled receptor 156 1385 rs903365 PPFIA4 8497 1 199776699 XM_046751 XP_046751 C/T C1347R plus 1335657 1303 SEQUENOM CEPH CEPH (92) 92 0.14 0.14 0 92 1 121 "by doubleHit,freq,cluster" radical 603145 1q32.1 "protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 4" 1386 rs906807 NDUFV2 4729 18 9107867 NM_021074 NP_066552 A/G V29A minus 1340074 1303 SEQUENOM CEPH CEPH (92) 92 0.23 0.23 0 92 1 121 "by doubleHit,submitter,freq" Benign 0.135 11 moderately conservative 600532 18p11.31-p11.2 "NADH dehydrogenase (ubiquinone) flavoprotein 2, 24kDa" 1387 rs910397 PXMP4 11264 20 31759202 NM_007238 NP_009169 C/T V204I plus 1344491 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 42 0.5 0.43 0.06 182 3 0.28 0.15 262 4 123 "by doubleHit,submitter,freq,cluster" Borderline 1.018 6 conservative 20q11.22 "peroxisomal membrane protein 4, 24kDa" 1388 rs910397 PXMP4 11264 20 31759202 NM_007238 NP_009169 C/T V204I plus 8372329 1303 SEQUENOM CEPH CEPH (92) 92 0.38 0.43 0.06 182 3 0.28 0.15 262 4 123 "by doubleHit,submitter,freq,cluster" Borderline 1.018 6 conservative 20q11.22 "peroxisomal membrane protein 4, 24kDa" 1389 rs910397 PXMP4 11264 20 31759202 NM_007238 NP_009169 C/T V204I plus 24537183 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.46 0.43 0.06 182 3 0.28 0.15 262 4 123 "by doubleHit,submitter,freq,cluster" Borderline 1.018 6 conservative 20q11.22 "peroxisomal membrane protein 4, 24kDa" 1390 rs915836 ZNF295 49854 21 42286430 NM_020727 NP_065778 C/T V282I plus 1351111 1303 SEQUENOM CEPH CEPH (92) 92 0.49 0.49 0 92 1 86 by freq conservative 21q22.3 zinc finger protein 295 1391 rs915843 ABCG1 9619 21 42552623 NM_207630 NP_997513 C/T P172L plus 4020640 634 PERLEGEN NCBI|NIHPDR NIHPDR 10 0.4 0.15 0.17 54 2 0.13 0.06 1576 3 123 "by doubleHit,submitter,freq,cluster" moderately conservative 603076 21q22.3 "ATP-binding cassette, sub-family G (WHITE), member 1" 1392 rs915843 ABCG1 9619 21 42552623 NM_207630 NP_997513 C/T P172L plus 23652333 1371 PERLEGEN AFD_EUR_PANEL European American (24) 44 0.09 0.15 0.17 54 2 0.13 0.06 1576 3 123 "by doubleHit,submitter,freq,cluster" moderately conservative 603076 21q22.3 "ATP-binding cassette, sub-family G (WHITE), member 1" 1393 rs917535 PCDHB11 56125 5 140559551 NM_018931 NP_061754 C/T R7H minus 1353203 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 82 0.01 0.05 0.05 222 3 0.12 0 120 2 123 "by doubleHit,submitter,freq,cluster" Benign 0.168 62 Tolerant 0.22 2.82 102 conservative 606337 5q31 protocadherin beta 11 1394 rs917535 PCDHB11 56125 5 140559551 NM_018931 NP_061754 C/T R7H minus 1353203 1303 SEQUENOM CEPH CEPH (92) 92 0.09 0.05 0.05 222 3 0.12 0 120 2 123 "by doubleHit,submitter,freq,cluster" Benign 0.168 62 Tolerant 0.22 2.82 102 conservative 606337 5q31 protocadherin beta 11 1395 rs917535 PCDHB11 56125 5 140559551 NM_018931 NP_061754 C/T R7H minus 23351567 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.05 0.05 222 3 0.12 0 120 2 123 "by doubleHit,submitter,freq,cluster" Benign 0.168 62 Tolerant 0.22 2.82 102 conservative 606337 5q31 protocadherin beta 11 1396 rs922697 SPON2 10417 4 1155571 NM_012445 NP_036577 A/G L40P plus 1359563 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 24 0.04 0.02 0.02 118 2 0.05 0 20 1 121 "HapMap,cluster" Benign 0.519 10 moderately conservative 605918 4p16.3 "spondin 2, extracellular matrix protein" 1397 rs922697 SPON2 10417 4 1155571 NM_012445 NP_036577 A/G L40P plus 1359563 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 94 0.01 0.02 0.02 118 2 0.05 0 20 1 121 "HapMap,cluster" Benign 0.519 10 moderately conservative 605918 4p16.3 "spondin 2, extracellular matrix protein" 1398 rs929387 GLI3 2737 7 41778918 NM_000168 NP_000159 C/T P998L minus 23376218 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.33 0.33 0 46 1 0.25 0.13 88 2 123 "by doubleHit,freq,cluster" Benign 0.2 7 moderately conservative 165240 7p13 GLI-Kruppel family member GLI3 (Greig cephalopolysyndactyly syndrome) 1399 rs930337 SORD 6652 15 43151826 NM_003104 NP_003095 A/C N269T plus 5252928 1303 SEQUENOM CEPH CEPH (92) 92 0.05 0.05 0 276 2 123 "by submitter,freq,cluster" Possibly damaging 1.764 25 moderately conservative 182500 15q15.3 sorbitol dehydrogenase 1400 rs930337 SORD 6652 15 43151826 NM_003104 NP_003095 A/C N269T plus 24802709 1303 SEQUENOM CEPH CEPH (92) 184 0.05 0.05 0 276 2 123 "by submitter,freq,cluster" Possibly damaging 1.764 25 moderately conservative 182500 15q15.3 sorbitol dehydrogenase 1401 rs933135 PLCD1 5333 3 38027729 NM_006225 NP_006216 C/T R257H plus 1372137 765 TSC-CSHL MOT_CAUCASIAN_CEPH MOTOROLA CEPH Caucasians (637) 320 0.02 0.02 0.01 438 3 0.19 0.02 84 2 111 by freq Potentially damaging 1.461 17 Potentially intolerant 0.08 2.77 40 conservative 602142 3p22-p21.3 "phospholipase C, delta 1" 1402 rs933135 PLCD1 5333 3 38027729 NM_006225 NP_006216 C/T R257H plus 1372137 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 24 0.04 0.02 0.01 438 3 0.19 0.02 84 2 111 by freq Potentially damaging 1.461 17 Potentially intolerant 0.08 2.77 40 conservative 602142 3p22-p21.3 "phospholipase C, delta 1" 1403 rs933135 PLCD1 5333 3 38027729 NM_006225 NP_006216 C/T R257H plus 1372137 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 94 0.02 0.02 0.01 438 3 0.19 0.02 84 2 111 by freq Potentially damaging 1.461 17 Potentially intolerant 0.08 2.77 40 conservative 602142 3p22-p21.3 "phospholipase C, delta 1" 1404 rs934945 PER2 8864 2 238937053 NM_022817 NP_073728 A/G G1244E minus 1374311 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.14 0.18 0.07 226 3 0.13 0.08 40 2 86 "HapMap,submitter,freq" moderately conservative 603426 2q37.3 period homolog 2 (Drosophila) 1405 rs934945 PER2 8864 2 238937053 NM_022817 NP_073728 A/G G1244E minus 1374311 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.13 0.18 0.07 226 3 0.13 0.08 40 2 86 "HapMap,submitter,freq" moderately conservative 603426 2q37.3 period homolog 2 (Drosophila) 1406 rs934945 PER2 8864 2 238937053 NM_022817 NP_073728 A/G G1244E minus 1374311 1303 SEQUENOM CEPH CEPH (92) 92 0.25 0.18 0.07 226 3 0.13 0.08 40 2 86 "HapMap,submitter,freq" moderately conservative 603426 2q37.3 period homolog 2 (Drosophila) 1407 rs937838 TGM4 7047 3 44918108 NM_003241 NP_003232 C/G S249T plus 1377860 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.21 0.2 0.04 198 3 0.04 0 1526 2 100 "by cluster,freq" Intolerant 0 2.78 17 moderately conservative 600585 3p22-p21.33 transglutaminase 4 (prostate) 1408 rs937838 TGM4 7047 3 44918108 NM_003241 NP_003232 C/G S249T plus 1377860 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 92 0.17 0.2 0.04 198 3 0.04 0 1526 2 100 "by cluster,freq" Intolerant 0 2.78 17 moderately conservative 600585 3p22-p21.33 transglutaminase 4 (prostate) 1409 rs937838 TGM4 7047 3 44918108 NM_003241 NP_003232 C/G S249T plus 1377860 1303 SEQUENOM CEPH CEPH (92) 92 0.23 0.2 0.04 198 3 0.04 0 1526 2 100 "by cluster,freq" Intolerant 0 2.78 17 moderately conservative 600585 3p22-p21.33 transglutaminase 4 (prostate) 1410 rs938886 TEP1 7011 14 19907541 NM_007110 NP_009041 C/G I2486M plus 1379184 760 TSC-CSHL CEL_CAUCASIAN CELERA Caucasians (30) 58 0.28 0.24 0.06 788 9 0.29 0.11 310 8 123 "HapMap,doubleHit,submitter,freq" conservative 601686 14q11.2 telomerase-associated protein 1 1411 rs938886 TEP1 7011 14 19907541 NM_007110 NP_009041 C/G I2486M plus 1379184 761 TSC-CSHL CEL_CAUCASIAN_CEPH CELERA CEPH Caucasians (661) 318 0.26 0.24 0.06 788 9 0.29 0.11 310 8 123 "HapMap,doubleHit,submitter,freq" conservative 601686 14q11.2 telomerase-associated protein 1 1412 rs938886 TEP1 7011 14 19907541 NM_007110 NP_009041 C/G I2486M plus 1379184 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 10 0.2 0.24 0.06 788 9 0.29 0.11 310 8 123 "HapMap,doubleHit,submitter,freq" conservative 601686 14q11.2 telomerase-associated protein 1 1413 rs938886 TEP1 7011 14 19907541 NM_007110 NP_009041 C/G I2486M plus 1379184 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.25 0.24 0.06 788 9 0.29 0.11 310 8 123 "HapMap,doubleHit,submitter,freq" conservative 601686 14q11.2 telomerase-associated protein 1 1414 rs938886 TEP1 7011 14 19907541 NM_007110 NP_009041 C/G I2486M plus 1379184 1303 SEQUENOM CEPH CEPH (92) 92 0.09 0.24 0.06 788 9 0.29 0.11 310 8 123 "HapMap,doubleHit,submitter,freq" conservative 601686 14q11.2 telomerase-associated protein 1 1415 rs938886 TEP1 7011 14 19907541 NM_007110 NP_009041 C/G I2486M plus 2549686 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.29 0.24 0.06 788 9 0.29 0.11 310 8 123 "HapMap,doubleHit,submitter,freq" conservative 601686 14q11.2 telomerase-associated protein 1 1416 rs938886 TEP1 7011 14 19907541 NM_007110 NP_009041 C/G I2486M plus 2549686 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 94 0.29 0.24 0.06 788 9 0.29 0.11 310 8 123 "HapMap,doubleHit,submitter,freq" conservative 601686 14q11.2 telomerase-associated protein 1 1417 rs938886 TEP1 7011 14 19907541 NM_007110 NP_009041 C/G I2486M plus 3172659 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 34 0.26 0.24 0.06 788 9 0.29 0.11 310 8 123 "HapMap,doubleHit,submitter,freq" conservative 601686 14q11.2 telomerase-associated protein 1 1418 rs938886 TEP1 7011 14 19907541 NM_007110 NP_009041 C/G I2486M plus 23814904 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.25 0.24 0.06 788 9 0.29 0.11 310 8 123 "HapMap,doubleHit,submitter,freq" conservative 601686 14q11.2 telomerase-associated protein 1 1419 rs940389 SBLF 11037 2 48719803 NM_006873 NP_006864 C/G R127T plus 1380968 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.38 0.41 0.04 260 3 0.4 0.02 1578 3 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 605357 2p16.3 stoned B-like factor 1420 rs940389 SBLF 11037 2 48719803 NM_006873 NP_006864 C/G R127T plus 1380968 1303 SEQUENOM CEPH CEPH (92) 92 0.45 0.41 0.04 260 3 0.4 0.02 1578 3 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 605357 2p16.3 stoned B-like factor 1421 rs940389 SBLF 11037 2 48719803 NM_006873 NP_006864 C/G R127T plus 24156949 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.42 0.41 0.04 260 3 0.4 0.02 1578 3 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 605357 2p16.3 stoned B-like factor 1422 rs947894 GSTP1 2950 11 67109265 NM_000852 NP_000843 A/G I105V plus 1390210 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.39 0.39 0.04 480 5 0.36 0.08 1028 7 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.129 26 Tolerant 0.9 2.8 39 conservative 134660 11q13 glutathione S-transferase pi 1423 rs947894 GSTP1 2950 11 67109265 NM_000852 NP_000843 A/G I105V plus 1390210 1303 SEQUENOM CEPH CEPH (92) 92 0.42 0.39 0.04 480 5 0.36 0.08 1028 7 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.129 26 Tolerant 0.9 2.8 39 conservative 134660 11q13 glutathione S-transferase pi 1424 rs947894 GSTP1 2950 11 67109265 NM_000852 NP_000843 A/G I105V plus 5586573 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.31 0.39 0.04 480 5 0.36 0.08 1028 7 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.129 26 Tolerant 0.9 2.8 39 conservative 134660 11q13 glutathione S-transferase pi 1425 rs947894 GSTP1 2950 11 67109265 NM_000852 NP_000843 A/G I105V plus 12585355 693 EGP_SNPS PDR90 NIHPDR 160 0.4 0.39 0.04 480 5 0.36 0.08 1028 7 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.129 26 Tolerant 0.9 2.8 39 conservative 134660 11q13 glutathione S-transferase pi 1426 rs947894 GSTP1 2950 11 67109265 NM_000852 NP_000843 A/G I105V plus 23600037 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.37 0.39 0.04 480 5 0.36 0.08 1028 7 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.129 26 Tolerant 0.9 2.8 39 conservative 134660 11q13 glutathione S-transferase pi 1427 rs948615 ZNF407 55628 18 70474878 NM_017757 NP_060227 G/T N158T minus 1391313 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.14 0.15 0.01 226 3 0.28 0.25 40 2 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 18q23 zinc finger protein 407 1428 rs948615 ZNF407 55628 18 70474878 NM_017757 NP_060227 G/T N158T minus 1391313 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 92 0.16 0.15 0.01 226 3 0.28 0.25 40 2 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 18q23 zinc finger protein 407 1429 rs948615 ZNF407 55628 18 70474878 NM_017757 NP_060227 G/T N158T minus 1391313 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.15 0.15 0.01 226 3 0.28 0.25 40 2 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 18q23 zinc finger protein 407 1430 rs956748 TAF2 6873 8 120813530 NM_003184 NP_003175 C/T T1139A plus 1402079 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.09 0.06 0.04 260 3 0.45 0 44 1 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 604912 8q24.12 "TAF2 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 150kDa" 1431 rs956748 TAF2 6873 8 120813530 NM_003184 NP_003175 C/T T1139A plus 1402079 1303 SEQUENOM CEPH CEPH (92) 92 0.02 0.06 0.04 260 3 0.45 0 44 1 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 604912 8q24.12 "TAF2 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 150kDa" 1432 rs956748 TAF2 6873 8 120813530 NM_003184 NP_003175 C/T T1139A plus 23390318 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.06 0.04 260 3 0.45 0 44 1 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 604912 8q24.12 "TAF2 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 150kDa" 1433 rs956749 TAF2 6873 8 120813580 NM_003184 NP_003175 C/T S1122N plus 1402080 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.09 0.09 0.04 260 3 0.18 0 44 1 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 604912 8q24.12 "TAF2 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 150kDa" 1434 rs956749 TAF2 6873 8 120813580 NM_003184 NP_003175 C/T S1122N plus 1402080 1303 SEQUENOM CEPH CEPH (92) 92 0.13 0.09 0.04 260 3 0.18 0 44 1 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 604912 8q24.12 "TAF2 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 150kDa" 1435 rs956749 TAF2 6873 8 120813580 NM_003184 NP_003175 C/T S1122N plus 23390327 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.09 0.04 260 3 0.18 0 44 1 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 604912 8q24.12 "TAF2 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 150kDa" 1436 rs956868 PRKWNK1 65125 12 861173 NM_018979 NP_061852 A/C T1056P plus 1402227 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.07 0.16 0.07 424 7 0.19 0.07 238 7 123 "HapMap,doubleHit,freq,cluster" conservative 605232 12p13.3 "protein kinase, lysine deficient 1" 1437 rs956868 PRKWNK1 65125 12 861173 NM_018979 NP_061852 A/C T1056P plus 1402227 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 90 0.13 0.16 0.07 424 7 0.19 0.07 238 7 123 "HapMap,doubleHit,freq,cluster" conservative 605232 12p13.3 "protein kinase, lysine deficient 1" 1438 rs956868 PRKWNK1 65125 12 861173 NM_018979 NP_061852 A/C T1056P plus 1402227 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.11 0.16 0.07 424 7 0.19 0.07 238 7 123 "HapMap,doubleHit,freq,cluster" conservative 605232 12p13.3 "protein kinase, lysine deficient 1" 1439 rs956868 PRKWNK1 65125 12 861173 NM_018979 NP_061852 A/C T1056P plus 1402227 902 AFFY Caucasian 40 0.13 0.16 0.07 424 7 0.19 0.07 238 7 123 "HapMap,doubleHit,freq,cluster" conservative 605232 12p13.3 "protein kinase, lysine deficient 1" 1440 rs956868 PRKWNK1 65125 12 861173 NM_018979 NP_061852 A/C T1056P plus 1402227 904 AFFY CEPH 20 0.35 0.16 0.07 424 7 0.19 0.07 238 7 123 "HapMap,doubleHit,freq,cluster" conservative 605232 12p13.3 "protein kinase, lysine deficient 1" 1441 rs956868 PRKWNK1 65125 12 861173 NM_018979 NP_061852 A/C T1056P plus 1402227 1303 SEQUENOM CEPH CEPH (92) 92 0.24 0.16 0.07 424 7 0.19 0.07 238 7 123 "HapMap,doubleHit,freq,cluster" conservative 605232 12p13.3 "protein kinase, lysine deficient 1" 1442 rs956868 PRKWNK1 65125 12 861173 NM_018979 NP_061852 A/C T1056P plus 23344913 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.16 0.07 424 7 0.19 0.07 238 7 123 "HapMap,doubleHit,freq,cluster" conservative 605232 12p13.3 "protein kinase, lysine deficient 1" 1443 rs961360 R3HDM 23518 2 136227390 NM_015361 NP_056176 C/T M270V minus 1408202 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.08 0.11 0.07 262 4 0.47 0.06 1722 6 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 2q21.3 R3H domain (binds single-stranded nucleic acids) containing 1444 rs961360 R3HDM 23518 2 136227390 NM_015361 NP_056176 C/T M270V minus 1408202 902 AFFY Caucasian 40 0.18 0.11 0.07 262 4 0.47 0.06 1722 6 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 2q21.3 R3H domain (binds single-stranded nucleic acids) containing 1445 rs961360 R3HDM 23518 2 136227390 NM_015361 NP_056176 C/T M270V minus 1408202 904 AFFY CEPH 54 0.2 0.11 0.07 262 4 0.47 0.06 1722 6 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 2q21.3 R3H domain (binds single-stranded nucleic acids) containing 1446 rs961360 R3HDM 23518 2 136227390 NM_015361 NP_056176 C/T M270V minus 23874392 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.11 0.07 262 4 0.47 0.06 1722 6 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 2q21.3 R3H domain (binds single-stranded nucleic acids) containing 1447 rs963075 SERPINB10 5273 18 59751364 NM_005024 NP_005015 A/G R246C minus 1410472 766 TSC-CSHL WICGR1_CAUCASIAN WICGR Caucasian (93) 86 0.21 0.26 0.05 454 6 0.36 0.02 1570 5 123 "HapMap,submitter,freq,cluster" Intolerant 0.04 2.87 56 radical 602058 18q21.3 "serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 10" 1448 rs963075 SERPINB10 5273 18 59751364 NM_005024 NP_005015 A/G R246C minus 1410472 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.21 0.26 0.05 454 6 0.36 0.02 1570 5 123 "HapMap,submitter,freq,cluster" Intolerant 0.04 2.87 56 radical 602058 18q21.3 "serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 10" 1449 rs963075 SERPINB10 5273 18 59751364 NM_005024 NP_005015 A/G R246C minus 1410472 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 94 0.23 0.26 0.05 454 6 0.36 0.02 1570 5 123 "HapMap,submitter,freq,cluster" Intolerant 0.04 2.87 56 radical 602058 18q21.3 "serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 10" 1450 rs963075 SERPINB10 5273 18 59751364 NM_005024 NP_005015 A/G R246C minus 1410472 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.3 0.26 0.05 454 6 0.36 0.02 1570 5 123 "HapMap,submitter,freq,cluster" Intolerant 0.04 2.87 56 radical 602058 18q21.3 "serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 10" 1451 rs963075 SERPINB10 5273 18 59751364 NM_005024 NP_005015 A/G R246C minus 1410472 1303 SEQUENOM CEPH CEPH (92) 92 0.33 0.26 0.05 454 6 0.36 0.02 1570 5 123 "HapMap,submitter,freq,cluster" Intolerant 0.04 2.87 56 radical 602058 18q21.3 "serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 10" 1452 rs963075 SERPINB10 5273 18 59751364 NM_005024 NP_005015 A/G R246C minus 24058834 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.23 0.26 0.05 454 6 0.36 0.02 1570 5 123 "HapMap,submitter,freq,cluster" Intolerant 0.04 2.87 56 radical 602058 18q21.3 "serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 10" 1453 rs964307 PKHD1L1 93035 8 110482938 NM_177531 NP_803875 A/G Y440H minus 1412128 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.22 0.27 0.08 197 4 0.36 0.16 158 5 123 "HapMap,submitter,freq,cluster" moderately conservative 607843 8q23.2 polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1 1454 rs964307 PKHD1L1 93035 8 110482938 NM_177531 NP_803875 A/G Y440H minus 1412128 902 AFFY Caucasian 24 0.38 0.27 0.08 197 4 0.36 0.16 158 5 123 "HapMap,submitter,freq,cluster" moderately conservative 607843 8q23.2 polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1 1455 rs964307 PKHD1L1 93035 8 110482938 NM_177531 NP_803875 A/G Y440H minus 1412128 904 AFFY CEPH 5 0.5 0.27 0.08 197 4 0.36 0.16 158 5 123 "HapMap,submitter,freq,cluster" moderately conservative 607843 8q23.2 polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1 1456 rs964307 PKHD1L1 93035 8 110482938 NM_177531 NP_803875 A/G Y440H minus 24083373 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.33 0.27 0.08 197 4 0.36 0.16 158 5 123 "HapMap,submitter,freq,cluster" moderately conservative 607843 8q23.2 polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1 1457 rs966365 EDARADD 128178 1 232883812 NM_145861 NP_665860 C/T M9I minus 1414869 760 TSC-CSHL CEL_CAUCASIAN CELERA Caucasians (30) 58 0.07 0.15 0.04 500 3 0.23 0.25 112 2 86 "HapMap,doubleHit,submitter,freq" conservative 606603 1q42.3 EDAR-associated death domain 1458 rs966365 EDARADD 128178 1 232883812 NM_145861 NP_665860 C/T M9I minus 1414869 761 TSC-CSHL CEL_CAUCASIAN_CEPH CELERA CEPH Caucasians (661) 322 0.16 0.15 0.04 500 3 0.23 0.25 112 2 86 "HapMap,doubleHit,submitter,freq" conservative 606603 1q42.3 EDAR-associated death domain 1459 rs966365 EDARADD 128178 1 232883812 NM_145861 NP_665860 C/T M9I minus 1414869 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.18 0.15 0.04 500 3 0.23 0.25 112 2 86 "HapMap,doubleHit,submitter,freq" conservative 606603 1q42.3 EDAR-associated death domain 1460 rs967185 EIF3S10 8661 10 120810797 NM_003750 NP_003741 C/T E386K plus 1415941 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 12 0.08 0.08 0 12 1 0.14 0 14 1 86 by freq Potentially damaging 1.267 13 Borderline 0.13 2.88 25 moderately conservative 602039 10q26 "eukaryotic translation initiation factor 3, subunit 10 theta, 150/170kDa" 1461 rs968457 IRF3 3661 19 54858462 NM_001571 NP_001562 A/G R96Q minus 3177821 619 WICVAR MITOGPOP6 CORIELL Mixed 48 0.06 0.06 0 48 1 123 by freq Borderline 1.137 5 Borderline 0.18 2.82 25 conservative 603734 19q13.3-q13.4 interferon regulatory factor 3 1462 rs984274 DCC 1630 18 49190933 NM_005215 NP_005206 C/T M1017V minus 3176064 619 WICVAR MITOGPOP6 CORIELL Mixed 34 0.06 0.06 0 34 1 0.27 0 44 1 123 "HapMap,submitter,freq,cluster" Benign 0.131 6 Tolerant 0.47 2.79 27 conservative 120470 18q21.3 deleted in colorectal carcinoma 1463 rs988574 ITGA1 3672 5 52276567 NM_181501 NP_852478 A/G E1108G plus 1444359 1303 SEQUENOM CEPH CEPH (92) 92 0.04 0.03 0.01 140 2 0.2 0.03 1586 3 123 "HapMap,submitter,freq,cluster" Tolerant 0.28 2.76 17 moderately conservative 192968 5q11.2 "integrin, alpha 1" 1464 rs988574 ITGA1 3672 5 52276567 NM_181501 NP_852478 A/G E1108G plus 23403789 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.03 0.01 140 2 0.2 0.03 1586 3 123 "HapMap,submitter,freq,cluster" Tolerant 0.28 2.76 17 moderately conservative 192968 5q11.2 "integrin, alpha 1" 1465 rs997983 MKI67 4288 10 129800465 NM_002417 NP_002408 A/C I631L minus 1456739 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 86 0.09 0.07 0.03 346 4 0.07 0.03 110 3 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 176741 10q25-qter antigen identified by monoclonal antibody Ki-67 1466 rs997983 MKI67 4288 10 129800465 NM_002417 NP_002408 A/C I631L minus 1456739 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.07 0.07 0.03 346 4 0.07 0.03 110 3 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 176741 10q25-qter antigen identified by monoclonal antibody Ki-67 1467 rs997983 MKI67 4288 10 129800465 NM_002417 NP_002408 A/C I631L minus 1456739 1303 SEQUENOM CEPH CEPH (92) 92 0.03 0.07 0.03 346 4 0.07 0.03 110 3 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 176741 10q25-qter antigen identified by monoclonal antibody Ki-67 1468 rs997983 MKI67 4288 10 129800465 NM_002417 NP_002408 A/C I631L minus 24598816 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.07 0.03 346 4 0.07 0.03 110 3 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 176741 10q25-qter antigen identified by monoclonal antibody Ki-67 1469 rs998532 TTF2 8458 1 117329747 NM_003594 NP_003585 A/G K167E plus 1457444 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 84 0.45 0.42 0.03 224 3 0.26 0.02 176 3 123 "by doubleHit,submitter,freq,cluster" moderately conservative 604718 1p22 "transcription termination factor, RNA polymerase II" 1470 rs998532 TTF2 8458 1 117329747 NM_003594 NP_003585 A/G K167E plus 1457444 1303 SEQUENOM CEPH CEPH (92) 92 0.39 0.42 0.03 224 3 0.26 0.02 176 3 123 "by doubleHit,submitter,freq,cluster" moderately conservative 604718 1p22 "transcription termination factor, RNA polymerase II" 1471 rs998532 TTF2 8458 1 117329747 NM_003594 NP_003585 A/G K167E plus 24265327 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.44 0.42 0.03 224 3 0.26 0.02 176 3 123 "by doubleHit,submitter,freq,cluster" moderately conservative 604718 1p22 "transcription termination factor, RNA polymerase II" 1472 rs999597 KRTAP13-4 284827 21 30724925 NM_181600 NP_853631 C/T R154H minus 1459029 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 84 0.02 0.03 0.01 204 2 86 "HapMap,freq" Benign 0.081 7 Borderline 0.11 3.18 11 conservative 21q22.1 keratin associated protein 13-4 1473 rs999597 KRTAP13-4 284827 21 30724925 NM_181600 NP_853631 C/T R154H minus 1459029 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.03 0.03 0.01 204 2 86 "HapMap,freq" Benign 0.081 7 Borderline 0.11 3.18 11 conservative 21q22.1 keratin associated protein 13-4 1474 rs999765 EPHA8 2046 1 22669179 NM_020526 NP_065387 C/G E612Q minus 1459261 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 84 0.1 0.1 0.02 224 3 0.09 0.04 258 4 123 "by doubleHit,freq" Benign 0.109 74 Intolerant 0 2.78 83 conservative 176945 1p36.11 EphA8 1475 rs999765 EPHA8 2046 1 22669179 NM_020526 NP_065387 C/G E612Q minus 1459261 1303 SEQUENOM CEPH CEPH (92) 92 0.11 0.1 0.02 224 3 0.09 0.04 258 4 123 "by doubleHit,freq" Benign 0.109 74 Intolerant 0 2.78 83 conservative 176945 1p36.11 EphA8 1476 rs999765 EPHA8 2046 1 22669179 NM_020526 NP_065387 C/G E612Q minus 23181480 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.1 0.02 224 3 0.09 0.04 258 4 123 "by doubleHit,freq" Benign 0.109 74 Intolerant 0 2.78 83 conservative 176945 1p36.11 EphA8 1477 rs999890 PIP5K3 200576 2 209016138 NM_015040 NP_055855 G/T S1033A plus 23215775 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.33 0.18 232 2 0.13 0 46 1 123 "by doubleHit,freq,cluster" moderately conservative 2q34 "phosphatidylinositol-3-phosphate/phosphatidylinositol 5-kinase, type III" 1478 rs999890 PIP5K3 200576 2 209016138 NM_015040 NP_055855 G/T S1033A plus 24795931 1303 SEQUENOM CEPH CEPH (92) 184 0.39 0.33 0.18 232 2 0.13 0 46 1 123 "by doubleHit,freq,cluster" moderately conservative 2q34 "phosphatidylinositol-3-phosphate/phosphatidylinositol 5-kinase, type III" 1479 rs1004041 TPSG1 25823 16 1211891 NM_012467 NP_036599 A/C F288L minus 1465449 1303 SEQUENOM CEPH CEPH (92) 92 0.32 0.35 0.07 140 2 0.28 0.13 94 2 123 "by doubleHit,freq,cluster" conservative 16p13.3 tryptase gamma 1 1480 rs1004041 TPSG1 25823 16 1211891 NM_012467 NP_036599 A/C F288L minus 24400155 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.42 0.35 0.07 140 2 0.28 0.13 94 2 123 "by doubleHit,freq,cluster" conservative 16p13.3 tryptase gamma 1 1481 rs1004588 DGKG 1608 3 187489320 NM_001346 NP_001337 C/G T142S minus 1466101 1303 SEQUENOM CEPH CEPH (92) 92 0.48 0.42 0.17 118 2 0.34 0 1300 1 102 "by doubleHit,freq,cluster" Benign 0.985 6 moderately conservative 601854 3q27-q28 "diacylglycerol kinase, gamma 90kDa" 1482 rs1004588 DGKG 1608 3 187489320 NM_001346 NP_001337 C/G T142S minus 3175901 619 WICVAR MITOGPOP6 CORIELL Mixed 26 0.19 0.42 0.17 118 2 0.34 0 1300 1 102 "by doubleHit,freq,cluster" Benign 0.985 6 moderately conservative 601854 3q27-q28 "diacylglycerol kinase, gamma 90kDa" 1483 rs1007211 NTRK1 4914 1 153643852 NM_002529 NP_002520 A/G G18E plus 1469256 1303 SEQUENOM CEPH CEPH (92) 92 0.08 0.08 0 92 1 86 by freq moderately conservative 191315 1q21-q22 "neurotrophic tyrosine kinase, receptor, type 1" 1484 rs1009382 TNXB 7148 6 32134085 NM_019105 NP_061978 A/G G2578E minus 1471878 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.38 0.35 0.06 212 2 0.32 0 1488 1 119 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.757 5 moderately conservative 600985 6p21.3 tenascin XB 1485 rs1009382 TNXB 7148 6 32134085 NM_019105 NP_061978 A/G G2578E minus 1471878 1303 SEQUENOM CEPH CEPH (92) 92 0.3 0.35 0.06 212 2 0.32 0 1488 1 119 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.757 5 moderately conservative 600985 6p21.3 tenascin XB 1486 rs1011320 PIK3R2 5296 19 18134047 NM_005027 NP_005018 C/T S313P plus 1474167 760 TSC-CSHL CEL_CAUCASIAN CELERA Caucasians (30) 60 0.05 0.06 0.03 320 4 0.04 0.02 118 2 121 "HapMap,doubleHit,freq,cluster" Benign 0.629 6 moderately conservative 603157 19q13.2-q13.4 "phosphoinositide-3-kinase, regulatory subunit, polypeptide 2 (p85 beta)" 1487 rs1011320 PIK3R2 5296 19 18134047 NM_005027 NP_005018 C/T S313P plus 1474167 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.08 0.06 0.03 320 4 0.04 0.02 118 2 121 "HapMap,doubleHit,freq,cluster" Benign 0.629 6 moderately conservative 603157 19q13.2-q13.4 "phosphoinositide-3-kinase, regulatory subunit, polypeptide 2 (p85 beta)" 1488 rs1011320 PIK3R2 5296 19 18134047 NM_005027 NP_005018 C/T S313P plus 1474167 1303 SEQUENOM CEPH CEPH (92) 92 0.02 0.06 0.03 320 4 0.04 0.02 118 2 121 "HapMap,doubleHit,freq,cluster" Benign 0.629 6 moderately conservative 603157 19q13.2-q13.4 "phosphoinositide-3-kinase, regulatory subunit, polypeptide 2 (p85 beta)" 1489 rs1011320 PIK3R2 5296 19 18134047 NM_005027 NP_005018 C/T S313P plus 3177906 619 WICVAR MITOGPOP6 CORIELL Mixed 50 0.08 0.06 0.03 320 4 0.04 0.02 118 2 121 "HapMap,doubleHit,freq,cluster" Benign 0.629 6 moderately conservative 603157 19q13.2-q13.4 "phosphoinositide-3-kinase, regulatory subunit, polypeptide 2 (p85 beta)" 1490 rs1017219 KCNA7 3743 19 54265250 NM_031886 NP_114092 A/G M418T plus 1481085 1303 SEQUENOM CEPH CEPH (92) 92 0.18 0.21 0.07 138 2 0.39 0.08 92 2 123 "by doubleHit,submitter,freq,cluster" Potentially damaging 1.293 31 moderately conservative 176268 19q13.3 "potassium voltage-gated channel, shaker-related subfamily, member 7" 1491 rs1017219 KCNA7 3743 19 54265250 NM_031886 NP_114092 A/G M418T plus 23812958 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.28 0.21 0.07 138 2 0.39 0.08 92 2 123 "by doubleHit,submitter,freq,cluster" Potentially damaging 1.293 31 moderately conservative 176268 19q13.3 "potassium voltage-gated channel, shaker-related subfamily, member 7" 1492 rs1017842 BUB1B 701 15 38276149 NM_001211 NP_001202 C/G E390D minus 23454880 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.02 0.02 0 46 1 0.11 0 46 1 123 "by cluster,freq" conservative 602860 15q15 BUB1 budding uninhibited by benzimidazoles 1 homolog beta (yeast) 1493 rs1018448 ARFGAP3 26286 22 41531448 NM_014570 NP_055385 A/C S355R plus 24550315 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.42 0.42 0 48 1 0.26 0.21 94 2 123 "by submitter,freq,cluster" Benign 0.478 18 moderately radical 22q13.2-q13.3 ADP-ribosylation factor GTPase activating protein 3 1494 rs1020694 SERPINB13 5275 18 59415278 NM_012397 NP_036529 C/T G293S minus 1484999 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.43 0.23 0.06 274 4 0.12 0.06 140 4 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.084 19 Tolerant 1 2.76 74 moderately conservative 604445 18q21.3-q22 "serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 13" 1495 rs1020694 SERPINB13 5275 18 59415278 NM_012397 NP_036529 C/T G293S minus 1484999 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 92 0.25 0.23 0.06 274 4 0.12 0.06 140 4 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.084 19 Tolerant 1 2.76 74 moderately conservative 604445 18q21.3-q22 "serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 13" 1496 rs1020694 SERPINB13 5275 18 59415278 NM_012397 NP_036529 C/T G293S minus 1484999 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.19 0.23 0.06 274 4 0.12 0.06 140 4 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.084 19 Tolerant 1 2.76 74 moderately conservative 604445 18q21.3-q22 "serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 13" 1497 rs1020694 SERPINB13 5275 18 59415278 NM_012397 NP_036529 C/T G293S minus 24494086 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.25 0.23 0.06 274 4 0.12 0.06 140 4 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.084 19 Tolerant 1 2.76 74 moderately conservative 604445 18q21.3-q22 "serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 13" 1498 rs1023783 LASS3 204219 15 98760568 NM_178842 NP_849164 C/T D342G plus 1488440 1303 SEQUENOM CEPH CEPH (92) 92 0.01 0.02 0.02 140 2 123 by freq Tolerant 0.39 2.92 11 moderately conservative 15q26.3 LAG1 longevity assurance homolog 3 (S. cerevisiae) 1499 rs1023783 LASS3 204219 15 98760568 NM_178842 NP_849164 C/T D342G plus 24594334 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.02 0.02 140 2 123 by freq Tolerant 0.39 2.92 11 moderately conservative 15q26.3 LAG1 longevity assurance homolog 3 (S. cerevisiae) 1500 rs1026128 COG1 9382 17 68708404 NM_018714 NP_061184 A/G N392S plus 24706885 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.42 0.42 0 48 1 0.37 0.01 1582 3 123 "by doubleHit,submitter,freq,cluster" Benign 0.242 5 Tolerant 0.46 2.92 7 conservative 606973 17q25.1 component of oligomeric golgi complex 1 1501 rs1027392 USP29 57663 19 62332958 NM_020903 NP_065954 A/G N368S plus 1492423 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 84 0.4 0.42 0.01 344 4 0.19 0.12 178 3 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 0.52 2.79 101 conservative 19q13.43 ubiquitin specific protease 29 1502 rs1027392 USP29 57663 19 62332958 NM_020903 NP_065954 A/G N368S plus 1492423 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.42 0.42 0.01 344 4 0.19 0.12 178 3 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 0.52 2.79 101 conservative 19q13.43 ubiquitin specific protease 29 1503 rs1027392 USP29 57663 19 62332958 NM_020903 NP_065954 A/G N368S plus 1492423 1303 SEQUENOM CEPH CEPH (92) 92 0.43 0.42 0.01 344 4 0.19 0.12 178 3 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 0.52 2.79 101 conservative 19q13.43 ubiquitin specific protease 29 1504 rs1027392 USP29 57663 19 62332958 NM_020903 NP_065954 A/G N368S plus 24719701 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.42 0.42 0.01 344 4 0.19 0.12 178 3 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 0.52 2.79 101 conservative 19q13.43 ubiquitin specific protease 29 1505 rs1029871 NEK4 6787 3 52772674 NM_003157 NP_003148 C/G P225A minus 1495161 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 10 0.1 0.29 0.13 216 4 0.3 0.16 132 4 123 "HapMap,doubleHit,submitter,freq" conservative 601959 3p21.1 NIMA (never in mitosis gene a)-related kinase 4 1506 rs1029871 NEK4 6787 3 52772674 NM_003157 NP_003148 C/G P225A minus 1495161 885 TSC-CSHL HapMap-CEPH-30-trios 102 0.3 0.29 0.13 216 4 0.3 0.16 132 4 123 "HapMap,doubleHit,submitter,freq" conservative 601959 3p21.1 NIMA (never in mitosis gene a)-related kinase 4 1507 rs1029871 NEK4 6787 3 52772674 NM_003157 NP_003148 C/G P225A minus 3177674 619 WICVAR MITOGPOP6 CORIELL Mixed 56 0.16 0.29 0.13 216 4 0.3 0.16 132 4 123 "HapMap,doubleHit,submitter,freq" conservative 601959 3p21.1 NIMA (never in mitosis gene a)-related kinase 4 1508 rs1029871 NEK4 6787 3 52772674 NM_003157 NP_003148 C/G P225A minus 24349523 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.46 0.29 0.13 216 4 0.3 0.16 132 4 123 "HapMap,doubleHit,submitter,freq" conservative 601959 3p21.1 NIMA (never in mitosis gene a)-related kinase 4 1509 rs1035539 BCAR1 9564 16 73834276 NM_014567 NP_055382 A/G P76S plus 1501489 1303 SEQUENOM CEPH CEPH (92) 92 0.13 0.13 0 92 1 0.38 0 1468 1 121 "by doubleHit,freq,cluster" Possibly damaging 1.8 6 Tolerant 0.23 3.04 11 moderately conservative 602941 16q22-q23 breast cancer anti-estrogen resistance 1 1510 rs1036199 HAVCR2 84868 5 156464314 NM_032782 NP_116171 A/C R140L plus 23304691 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.17 0.17 0 46 1 0.03 0.04 1548 2 123 "by cluster,freq" Borderline 0.2 2.93 21 moderately radical 606652 5q33.3 hepatitis A virus cellular receptor 2 1511 rs1037921 ARNTL2 56938 12 27444833 NM_020183 NP_064568 C/T N340S minus 1504123 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.07 0.04 0.03 260 3 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.03 11 Tolerant 0.59 2.89 85 conservative 12p12.2-p11.2 aryl hydrocarbon receptor nuclear translocator-like 2 1512 rs1037921 ARNTL2 56938 12 27444833 NM_020183 NP_064568 C/T N340S minus 1504123 1303 SEQUENOM CEPH CEPH (92) 92 0.02 0.04 0.03 260 3 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.03 11 Tolerant 0.59 2.89 85 conservative 12p12.2-p11.2 aryl hydrocarbon receptor nuclear translocator-like 2 1513 rs1037921 ARNTL2 56938 12 27444833 NM_020183 NP_064568 C/T N340S minus 24451963 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.04 0.03 260 3 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.03 11 Tolerant 0.59 2.89 85 conservative 12p12.2-p11.2 aryl hydrocarbon receptor nuclear translocator-like 2 1514 rs1040835 GOLGA5 9950 14 92346407 NM_005113 NP_005104 A/G F350L minus 1507380 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.33 0.3 0.06 260 3 0.15 0.03 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Potentially damaging 1.255 8 Tolerant 1 2.87 11 conservative 606918 14q32.12-q32.13 "golgi autoantigen, golgin subfamily a, 5" 1515 rs1040835 GOLGA5 9950 14 92346407 NM_005113 NP_005104 A/G F350L minus 1507380 1303 SEQUENOM CEPH CEPH (92) 92 0.23 0.3 0.06 260 3 0.15 0.03 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Potentially damaging 1.255 8 Tolerant 1 2.87 11 conservative 606918 14q32.12-q32.13 "golgi autoantigen, golgin subfamily a, 5" 1516 rs1040835 GOLGA5 9950 14 92346407 NM_005113 NP_005104 A/G F350L minus 24600610 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.35 0.3 0.06 260 3 0.15 0.03 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Potentially damaging 1.255 8 Tolerant 1 2.87 11 conservative 606918 14q32.12-q32.13 "golgi autoantigen, golgin subfamily a, 5" 1517 rs1041981 LTA 4049 6 31648763 NM_000595 NP_000586 A/C T60N plus 4328795 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 42 0.36 0.37 0.03 338 5 0.37 0.03 1596 4 123 "by doubleHit,freq,cluster" Benign 0.111 15 Tolerant 0.41 2.8 86 moderately conservative 153440 6p21.3 "lymphotoxin alpha (TNF superfamily, member 1)" 1518 rs1041981 LTA 4049 6 31648763 NM_000595 NP_000586 A/C T60N plus 6312883 693 EGP_SNPS PDR90 NIHPDR 172 0.38 0.37 0.03 338 5 0.37 0.03 1596 4 123 "by doubleHit,freq,cluster" Benign 0.111 15 Tolerant 0.41 2.8 86 moderately conservative 153440 6p21.3 "lymphotoxin alpha (TNF superfamily, member 1)" 1519 rs1041981 LTA 4049 6 31648763 NM_000595 NP_000586 A/C T60N plus 16360682 649 FHCRC POPU1 USA (20) 40 0.38 0.37 0.03 338 5 0.37 0.03 1596 4 123 "by doubleHit,freq,cluster" Benign 0.111 15 Tolerant 0.41 2.8 86 moderately conservative 153440 6p21.3 "lymphotoxin alpha (TNF superfamily, member 1)" 1520 rs1041981 LTA 4049 6 31648763 NM_000595 NP_000586 A/C T60N plus 16360732 649 FHCRC POPU1 USA (20) 40 0.38 0.37 0.03 338 5 0.37 0.03 1596 4 123 "by doubleHit,freq,cluster" Benign 0.111 15 Tolerant 0.41 2.8 86 moderately conservative 153440 6p21.3 "lymphotoxin alpha (TNF superfamily, member 1)" 1521 rs1041981 LTA 4049 6 31648763 NM_000595 NP_000586 A/C T60N plus 23323156 1371 PERLEGEN AFD_EUR_PANEL European American (24) 44 0.3 0.37 0.03 338 5 0.37 0.03 1596 4 123 "by doubleHit,freq,cluster" Benign 0.111 15 Tolerant 0.41 2.8 86 moderately conservative 153440 6p21.3 "lymphotoxin alpha (TNF superfamily, member 1)" 1522 rs1042007 DNM1 1759 9 128092101 NM_004408 NP_004399 A/G D744N plus 1508887 1303 SEQUENOM CEPH CEPH (92) 92 0.47 0.47 0 92 1 106 by freq Possibly damaging 1.593 37 conservative 602377 9q34 dynamin 1 1523 rs1042017 SREBF1 6720 17 17657712 NM_004176 NP_004167 A/G T1000A minus 1508900 1303 SEQUENOM CEPH CEPH (92) 92 0.45 0.45 0 92 1 86 by freq Benign 0.472 14 Tolerant 0.79 2.82 21 moderately conservative 184756 17p11.2 sterol regulatory element binding transcription factor 1 1524 rs1042031 APOB 338 2 21137405 NM_000384 NP_000375 A/G E4181K minus 6312533 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.21 0.19 0.02 260 3 0.23 0.12 602 5 123 "HapMap,freq,cluster" moderately conservative 107730 2p24-p23 apolipoprotein B (including Ag(x) antigen) 1525 rs1042031 APOB 338 2 21137405 NM_000384 NP_000375 A/G E4181K minus 6312533 1303 SEQUENOM CEPH CEPH (92) 92 0.18 0.19 0.02 260 3 0.23 0.12 602 5 123 "HapMap,freq,cluster" moderately conservative 107730 2p24-p23 apolipoprotein B (including Ag(x) antigen) 1526 rs1042031 APOB 338 2 21137405 NM_000384 NP_000375 A/G E4181K minus 24242162 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.17 0.19 0.02 260 3 0.23 0.12 602 5 123 "HapMap,freq,cluster" moderately conservative 107730 2p24-p23 apolipoprotein B (including Ag(x) antigen) 1527 rs1042034 APOB 338 2 21136933 NM_000384 NP_000375 A/G S4338N minus 3290027 1303 SEQUENOM CEPH CEPH (92) 92 0.14 0.18 0.04 202 3 0.26 0.09 528 7 123 "by doubleHit,freq,cluster" conservative 107730 2p24-p23 apolipoprotein B (including Ag(x) antigen) 1528 rs1042034 APOB 338 2 21136933 NM_000384 NP_000375 A/G S4338N minus 8819680 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.19 0.18 0.04 202 3 0.26 0.09 528 7 123 "by doubleHit,freq,cluster" conservative 107730 2p24-p23 apolipoprotein B (including Ag(x) antigen) 1529 rs1042034 APOB 338 2 21136933 NM_000384 NP_000375 A/G S4338N minus 23841045 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.23 0.18 0.04 202 3 0.26 0.09 528 7 123 "by doubleHit,freq,cluster" conservative 107730 2p24-p23 apolipoprotein B (including Ag(x) antigen) 1530 rs1042038 PSCDBP 9595 2 158125932 NM_004288 NP_004279 A/G D37N minus 1508934 1303 SEQUENOM CEPH CEPH (92) 92 0.2 0.2 0 92 1 86 by freq conservative 604448 2q11.2 "pleckstrin homology, Sec7 and coiled-coil domains, binding protein" 1531 rs1042057 TYRO3 7301 15 39657537 NM_006293 NP_006284 C/T A815V plus 1508967 1303 SEQUENOM CEPH CEPH (92) 92 0.04 0.04 0 92 1 86 by freq Borderline 1.048 10 Borderline 0.14 2.84 25 moderately conservative 600341 15q15.1-q21.1 TYRO3 protein tyrosine kinase 1532 rs1042206 FCGR3A 2214 1 158326014 NM_000569 NP_000560 C/T F239S minus 16417111 1303 SEQUENOM CEPH CEPH (92) 92 0.48 0.48 0 92 1 120 "by doubleHit,freq,cluster" Benign 0.982 20 Tolerant 0.22 3.03 30 radical 146740 1q23 "Fc fragment of IgG, low affinity IIIa, receptor for (CD16)" 1533 rs1042229 FPR1 2357 19 56941484 NM_002029 NP_002020 G/T N192K minus 14699224 1303 SEQUENOM CEPH CEPH (92) 92 0.48 0.48 0 92 1 0.42 0 1456 1 119 "by submitter,freq,cluster" Benign 0.032 28 Tolerant 0.92 2.94 30 moderately conservative 136537 19q13.4 formyl peptide receptor 1 1534 rs1042303 GPLD1 2822 6 24545437 NM_001503 NP_001494 C/T M694V plus 2632160 1303 SEQUENOM CEPH CEPH (92) 92 0.24 0.3 0.12 140 2 0.24 0.01 1582 3 123 "by doubleHit,freq,cluster" Borderline 1.001 10 Tolerant 0.53 2.98 38 conservative 602515 6p22.3-p22.2 glycosylphosphatidylinositol specific phospholipase D1 1535 rs1042303 GPLD1 2822 6 24545437 NM_001503 NP_001494 C/T M694V plus 24425828 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.42 0.3 0.12 140 2 0.24 0.01 1582 3 123 "by doubleHit,freq,cluster" Borderline 1.001 10 Tolerant 0.53 2.98 38 conservative 602515 6p22.3-p22.2 glycosylphosphatidylinositol specific phospholipase D1 1536 rs1042364 ADH4 127 4 100402752 NM_000670 NP_000661 A/G R388G minus 10157120 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.32 0.31 0.02 212 2 121 "HapMap,submitter,freq,cluster" moderately radical 103740 4q22 "alcohol dehydrogenase 4 (class II), pi polypeptide" 1537 rs1042364 ADH4 127 4 100402752 NM_000670 NP_000661 A/G R388G minus 10157120 1303 SEQUENOM CEPH CEPH (92) 92 0.29 0.31 0.02 212 2 121 "HapMap,submitter,freq,cluster" moderately radical 103740 4q22 "alcohol dehydrogenase 4 (class II), pi polypeptide" 1538 rs1042391 GMPR 2766 6 16398740 NM_006877 NP_006868 A/T F256I plus 10319972 885 TSC-CSHL HapMap-CEPH-30-trios 112 0.37 0.38 0.05 252 3 0.17 0.04 94 2 123 "HapMap,doubleHit,freq,cluster" Benign 0.509 38 conservative 139265 6p23 guanosine monophosphate reductase 1539 rs1042391 GMPR 2766 6 16398740 NM_006877 NP_006868 A/T F256I plus 10319972 1303 SEQUENOM CEPH CEPH (92) 92 0.43 0.38 0.05 252 3 0.17 0.04 94 2 123 "HapMap,doubleHit,freq,cluster" Benign 0.509 38 conservative 139265 6p23 guanosine monophosphate reductase 1540 rs1042391 GMPR 2766 6 16398740 NM_006877 NP_006868 A/T F256I plus 24374803 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.33 0.38 0.05 252 3 0.17 0.04 94 2 123 "HapMap,doubleHit,freq,cluster" Benign 0.509 38 conservative 139265 6p23 guanosine monophosphate reductase 1541 rs1042445 HRG 3273 3 187878138 NM_000412 NP_000403 C/T R448C plus 1509688 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.21 0.18 0.03 258 3 0.31 0.01 92 2 123 "HapMap,submitter,freq,cluster" radical 142640 3q27 histidine-rich glycoprotein 1542 rs1042445 HRG 3273 3 187878138 NM_000412 NP_000403 C/T R448C plus 1509688 1303 SEQUENOM CEPH CEPH (92) 92 0.15 0.18 0.03 258 3 0.31 0.01 92 2 123 "HapMap,submitter,freq,cluster" radical 142640 3q27 histidine-rich glycoprotein 1543 rs1042445 HRG 3273 3 187878138 NM_000412 NP_000403 C/T R448C plus 23287771 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.17 0.18 0.03 258 3 0.31 0.01 92 2 123 "HapMap,submitter,freq,cluster" radical 142640 3q27 histidine-rich glycoprotein 1544 rs1042464 HRG 3273 3 187878274 NM_000412 NP_000403 A/T N493I plus 3172905 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 52 0.37 0.35 0.06 222 5 0.29 0.1 158 5 123 "by doubleHit,freq,cluster" moderately radical 142640 3q27 histidine-rich glycoprotein 1545 rs1042464 HRG 3273 3 187878274 NM_000412 NP_000403 A/T N493I plus 10078370 902 AFFY Caucasian 22 0.41 0.35 0.06 222 5 0.29 0.1 158 5 123 "by doubleHit,freq,cluster" moderately radical 142640 3q27 histidine-rich glycoprotein 1546 rs1042464 HRG 3273 3 187878274 NM_000412 NP_000403 A/T N493I plus 10078370 904 AFFY CEPH 10 0.2 0.35 0.06 222 5 0.29 0.1 158 5 123 "by doubleHit,freq,cluster" moderately radical 142640 3q27 histidine-rich glycoprotein 1547 rs1042464 HRG 3273 3 187878274 NM_000412 NP_000403 A/T N493I plus 10078370 1303 SEQUENOM CEPH CEPH (92) 92 0.3 0.35 0.06 222 5 0.29 0.1 158 5 123 "by doubleHit,freq,cluster" moderately radical 142640 3q27 histidine-rich glycoprotein 1548 rs1042464 HRG 3273 3 187878274 NM_000412 NP_000403 A/T N493I plus 24333187 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.41 0.35 0.06 222 5 0.29 0.1 158 5 123 "by doubleHit,freq,cluster" moderately radical 142640 3q27 histidine-rich glycoprotein 1549 rs1042522 TP53 7157 17 7520197 NM_000546 NP_000537 C/G P72R minus 2463129 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.23 0.32 0.12 338 4 0.41 0.08 346 4 121 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.821 51 moderately radical 191170 17p13.1 tumor protein p53 (Li-Fraumeni syndrome) 1550 rs1042522 TP53 7157 17 7520197 NM_000546 NP_000537 C/G P72R minus 2463129 1303 SEQUENOM CEPH CEPH (92) 92 0.48 0.32 0.12 338 4 0.41 0.08 346 4 121 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.821 51 moderately radical 191170 17p13.1 tumor protein p53 (Li-Fraumeni syndrome) 1551 rs1042522 TP53 7157 17 7520197 NM_000546 NP_000537 C/G P72R minus 3176059 619 WICVAR MITOGPOP6 CORIELL Mixed 64 0.33 0.32 0.12 338 4 0.41 0.08 346 4 121 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.821 51 moderately radical 191170 17p13.1 tumor protein p53 (Li-Fraumeni syndrome) 1552 rs1042522 TP53 7157 17 7520197 NM_000546 NP_000537 C/G P72R minus 5586947 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.27 0.32 0.12 338 4 0.41 0.08 346 4 121 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.821 51 moderately radical 191170 17p13.1 tumor protein p53 (Li-Fraumeni syndrome) 1553 rs1042589 TPO 7173 2 1525334 NM_175720 NP_783651 C/G P918R plus 23877133 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.42 0.42 0 232 2 0.31 0.19 94 2 123 "by doubleHit,freq,cluster" moderately radical 606765 2p25 thyroid peroxidase 1554 rs1042589 TPO 7173 2 1525334 NM_175720 NP_783651 C/G P918R plus 24815828 1303 SEQUENOM CEPH CEPH (92) 184 0.42 0.42 0 232 2 0.31 0.19 94 2 123 "by doubleHit,freq,cluster" moderately radical 606765 2p25 thyroid peroxidase 1555 rs1042602 TYR 7299 11 88551344 NM_000372 NP_000363 A/C S192Y plus 1509962 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.42 0.42 0.08 369 5 0.05 0.03 282 4 123 "HapMap,freq" Possibly damaging 1.634 41 Intolerant 0 2.81 166 moderately radical 606933 11q14-q21 tyrosinase (oculocutaneous albinism IA) 1556 rs1042602 TYR 7299 11 88551344 NM_000372 NP_000363 A/C S192Y plus 1509962 1303 SEQUENOM CEPH CEPH (92) 92 0.47 0.42 0.08 369 5 0.05 0.03 282 4 123 "HapMap,freq" Possibly damaging 1.634 41 Intolerant 0 2.81 166 moderately radical 606933 11q14-q21 tyrosinase (oculocutaneous albinism IA) 1557 rs1042602 TYR 7299 11 88551344 NM_000372 NP_000363 A/C S192Y plus 4387030 705 PSU-ANTH GERMANY German 30 0.41 0.42 0.08 369 5 0.05 0.03 282 4 123 "HapMap,freq" Possibly damaging 1.634 41 Intolerant 0 2.81 166 moderately radical 606933 11q14-q21 tyrosinase (oculocutaneous albinism IA) 1558 rs1042602 TYR 7299 11 88551344 NM_000372 NP_000363 A/C S192Y plus 4387030 706 PSU-ANTH SPAIN Spanish 79 0.49 0.42 0.08 369 5 0.05 0.03 282 4 123 "HapMap,freq" Possibly damaging 1.634 41 Intolerant 0 2.81 166 moderately radical 606933 11q14-q21 tyrosinase (oculocutaneous albinism IA) 1559 rs1042602 TYR 7299 11 88551344 NM_000372 NP_000363 A/C S192Y plus 24427553 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.25 0.42 0.08 369 5 0.05 0.03 282 4 123 "HapMap,freq" Possibly damaging 1.634 41 Intolerant 0 2.81 166 moderately radical 606933 11q14-q21 tyrosinase (oculocutaneous albinism IA) 1560 rs1042636 CASR 846 3 123486459 NM_000388 NP_000379 A/G R990G plus 5606249 775 SNP500CANCER CAUC1 Caucasian (31) 60 0.07 0.08 0.04 200 3 0.39 0.13 1938 7 123 "by cluster,freq" Possibly damaging 1.575 6 moderately radical 601199 3q21-q24 "calcium-sensing receptor (hypocalciuric hypercalcemia 1, severe neonatal hyperparathyroidism)" 1561 rs1042636 CASR 846 3 123486459 NM_000388 NP_000379 A/G R990G plus 22030142 1303 SEQUENOM CEPH CEPH (92) 92 0.11 0.08 0.04 200 3 0.39 0.13 1938 7 123 "by cluster,freq" Possibly damaging 1.575 6 moderately radical 601199 3q21-q24 "calcium-sensing receptor (hypocalciuric hypercalcemia 1, severe neonatal hyperparathyroidism)" 1562 rs1042636 CASR 846 3 123486459 NM_000388 NP_000379 A/G R990G plus 23901762 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.08 0.04 200 3 0.39 0.13 1938 7 123 "by cluster,freq" Possibly damaging 1.575 6 moderately radical 601199 3q21-q24 "calcium-sensing receptor (hypocalciuric hypercalcemia 1, severe neonatal hyperparathyroidism)" 1563 rs1042703 MMP14 4323 14 22375888 NM_004995 NP_004986 C/T P8S plus 2414700 1303 SEQUENOM CEPH CEPH (92) 92 0.16 0.13 0.05 140 2 0.05 0.05 94 2 123 "by doubleHit,freq,cluster" moderately conservative 600754 14q11-q12 matrix metalloproteinase 14 (membrane-inserted) 1564 rs1042703 MMP14 4323 14 22375888 NM_004995 NP_004986 C/T P8S plus 23815139 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.13 0.05 140 2 0.05 0.05 94 2 123 "by doubleHit,freq,cluster" moderately conservative 600754 14q11-q12 matrix metalloproteinase 14 (membrane-inserted) 1565 rs1042704 MMP14 4323 14 22382434 NM_004995 NP_004986 A/G D273N plus 1510165 1303 SEQUENOM CEPH CEPH (92) 92 0.49 0.49 0 92 1 106 by freq Benign 0.344 33 Tolerant 0.41 2.83 48 conservative 600754 14q11-q12 matrix metalloproteinase 14 (membrane-inserted) 1566 rs1042779 ITIH1 3697 3 52796051 NM_002215 NP_002206 A/G Q595R plus 19520909 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.28 0.35 0.08 260 3 0.48 0.02 1564 3 123 "HapMap,doubleHit,freq,cluster" Borderline 1.147 19 conservative 147270 3p21.2-p21.1 inter-alpha (globulin) inhibitor H1 1567 rs1042779 ITIH1 3697 3 52796051 NM_002215 NP_002206 A/G Q595R plus 19520909 1303 SEQUENOM CEPH CEPH (92) 92 0.38 0.35 0.08 260 3 0.48 0.02 1564 3 123 "HapMap,doubleHit,freq,cluster" Borderline 1.147 19 conservative 147270 3p21.2-p21.1 inter-alpha (globulin) inhibitor H1 1568 rs1042779 ITIH1 3697 3 52796051 NM_002215 NP_002206 A/G Q595R plus 24349623 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.46 0.35 0.08 260 3 0.48 0.02 1564 3 123 "HapMap,doubleHit,freq,cluster" Borderline 1.147 19 conservative 147270 3p21.2-p21.1 inter-alpha (globulin) inhibitor H1 1569 rs1042780 ME3 10873 11 85839036 NM_006680 NP_006671 C/G K324N minus 1510291 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.34 0.37 0.06 212 2 120 "HapMap,submitter,freq" Benign 0.202 39 moderately conservative 604626 11cen-q22.3 "malic enzyme 3, NADP(+)-dependent, mitochondrial" 1570 rs1042780 ME3 10873 11 85839036 NM_006680 NP_006671 C/G K324N minus 1510291 1303 SEQUENOM CEPH CEPH (92) 92 0.42 0.37 0.06 212 2 120 "HapMap,submitter,freq" Benign 0.202 39 moderately conservative 604626 11cen-q22.3 "malic enzyme 3, NADP(+)-dependent, mitochondrial" 1571 rs1042821 MSH6 2956 2 47922139 NM_000179 NP_000170 C/T G39E minus 4384481 693 EGP_SNPS PDR90 NIHPDR 152 0.16 0.16 0 152 1 123 "by cluster,freq" Benign 0.06 7 moderately conservative 600678 2p16 mutS homolog 6 (E. coli) 1572 rs1042838 PGR 5241 11 100438622 NM_000926 NP_000917 G/T V660L minus 16343470 693 EGP_SNPS PDR90 NIHPDR 180 0.1 0.17 0.1 318 3 0.03 0.01 94 2 123 "by submitter,freq,cluster" Borderline 1.07 10 conservative 607311 11q22-q23 progesterone receptor 1573 rs1042838 PGR 5241 11 100438622 NM_000926 NP_000917 G/T V660L minus 16343470 1303 SEQUENOM CEPH CEPH (92) 92 0.27 0.17 0.1 318 3 0.03 0.01 94 2 123 "by submitter,freq,cluster" Borderline 1.07 10 conservative 607311 11q22-q23 progesterone receptor 1574 rs1042838 PGR 5241 11 100438622 NM_000926 NP_000917 G/T V660L minus 24586705 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.24 0.17 0.1 318 3 0.03 0.01 94 2 123 "by submitter,freq,cluster" Borderline 1.07 10 conservative 607311 11q22-q23 progesterone receptor 1575 rs1043261 IL17RB 55540 3 53874316 NM_018725 NP_061195 C/T Q484X plus 10050330 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.09 0.08 0.02 168 2 0.1 0.03 1570 3 123 "HapMap,doubleHit,freq,cluster" Probably damaging Intolerant radical 605458 3p21.1 interleukin 17 receptor B 1576 rs1043261 IL17RB 55540 3 53874316 NM_018725 NP_061195 C/T Q484X plus 23945774 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.08 0.02 168 2 0.1 0.03 1570 3 123 "HapMap,doubleHit,freq,cluster" Probably damaging Intolerant radical 605458 3p21.1 interleukin 17 receptor B 1577 rs1043307 PSMD9 5715 12 120816516 NM_002813 NP_002804 A/G E197G plus 1511360 1303 SEQUENOM CEPH CEPH (92) 92 0.19 0.22 0.05 140 2 0.29 0.28 90 2 123 "by cluster,freq" Possibly damaging 1.576 8 Borderline 0.16 2.91 13 moderately conservative 603146 12q24.31-q24.32 "proteasome (prosome, macropain) 26S subunit, non-ATPase, 9" 1578 rs1043307 PSMD9 5715 12 120816516 NM_002813 NP_002804 A/G E197G plus 23934828 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.27 0.22 0.05 140 2 0.29 0.28 90 2 123 "by cluster,freq" Possibly damaging 1.576 8 Borderline 0.16 2.91 13 moderately conservative 603146 12q24.31-q24.32 "proteasome (prosome, macropain) 26S subunit, non-ATPase, 9" 1579 rs1043424 PINK1 65018 1 20722306 NM_032409 NP_115785 A/C N521T plus 1511554 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.34 0.34 0.08 260 3 0.26 0.08 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Potentially damaging 1.319 8 Borderline 0.13 2.8 62 moderately conservative 608309 1p36 PTEN induced putative kinase 1 1580 rs1043424 PINK1 65018 1 20722306 NM_032409 NP_115785 A/C N521T plus 15414508 1303 SEQUENOM CEPH CEPH (92) 92 0.4 0.34 0.08 260 3 0.26 0.08 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Potentially damaging 1.319 8 Borderline 0.13 2.8 62 moderately conservative 608309 1p36 PTEN induced putative kinase 1 1581 rs1043424 PINK1 65018 1 20722306 NM_032409 NP_115785 A/C N521T plus 23842660 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.34 0.08 260 3 0.26 0.08 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Potentially damaging 1.319 8 Borderline 0.13 2.8 62 moderately conservative 608309 1p36 PTEN induced putative kinase 1 1582 rs1043963 USHBP1 83878 19 17222116 NM_031941 NP_114147 C/T A677V minus 1512609 1303 SEQUENOM CEPH CEPH (92) 92 0.31 0.31 0 92 1 120 by freq moderately conservative 19p13 Usher syndrome 1C binding protein 1 1583 rs1044009 NOTCH3 4854 19 15132771 NM_000435 NP_000426 C/T A2223V minus 2990861 1303 SEQUENOM CEPH CEPH (92) 92 0.3 0.27 0.06 140 2 0.4 0.02 1580 3 123 "by cluster,freq" moderately conservative 600276 19p13.2-p13.1 Notch homolog 3 (Drosophila) 1584 rs1044009 NOTCH3 4854 19 15132771 NM_000435 NP_000426 C/T A2223V minus 23538988 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.27 0.06 140 2 0.4 0.02 1580 3 123 "by cluster,freq" moderately conservative 600276 19p13.2-p13.1 Notch homolog 3 (Drosophila) 1585 rs1044057 STX7 8417 6 132866329 NM_003569 NP_003560 A/G A12T minus 1512787 1303 SEQUENOM CEPH CEPH (92) 92 0.24 0.24 0 92 1 86 by freq Benign 0.667 16 moderately conservative 603217 6q23.1 syntaxin 7 1586 rs1044141 STK17A 9263 7 43437520 NM_004760 NP_004751 A/G K362E plus 10414990 1303 SEQUENOM CEPH CEPH (92) 92 0.44 0.37 0.13 140 2 0.28 0.05 1580 3 123 "by doubleHit,freq,cluster" Borderline 1.053 5 moderately conservative 604726 7p12-p14 serine/threonine kinase 17a (apoptosis-inducing) 1587 rs1044141 STK17A 9263 7 43437520 NM_004760 NP_004751 A/G K362E plus 23968531 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.25 0.37 0.13 140 2 0.28 0.05 1580 3 123 "by doubleHit,freq,cluster" Borderline 1.053 5 moderately conservative 604726 7p12-p14 serine/threonine kinase 17a (apoptosis-inducing) 1588 rs1044240 ALCAM 214 3 106741551 NM_001627 NP_001618 A/G N258S plus 24796196 1303 SEQUENOM CEPH CEPH (92) 184 0.16 0.16 0 184 1 123 by freq Benign 0.226 12 Tolerant 1 2.79 21 conservative 601662 3q13.1 activated leukocyte cell adhesion molecule 1589 rs1044243 ALCAM 214 3 106743210 NM_001627 NP_001618 C/T T301M plus 14169589 1303 SEQUENOM CEPH CEPH (92) 92 0.24 0.19 0.09 140 2 0.06 0.03 86 2 123 "by cluster,freq" Possibly damaging 1.873 12 moderately conservative 601662 3q13.1 activated leukocyte cell adhesion molecule 1590 rs1044243 ALCAM 214 3 106743210 NM_001627 NP_001618 C/T T301M plus 24308750 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.19 0.09 140 2 0.06 0.03 86 2 123 "by cluster,freq" Possibly damaging 1.873 12 moderately conservative 601662 3q13.1 activated leukocyte cell adhesion molecule 1591 rs1044261 IDI2 91734 10 1055710 NM_033261 NP_150286 C/T W144X plus 12109295 1303 SEQUENOM CEPH CEPH (92) 92 0.15 0.13 0.05 140 2 0.07 0 44 1 123 "by cluster,freq" Probably damaging Intolerant radical 10p15.3 isopentenyl-diphosphate delta isomerase 2 1592 rs1044261 IDI2 91734 10 1055710 NM_033261 NP_150286 C/T W144X plus 24623784 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.13 0.05 140 2 0.07 0 44 1 123 "by cluster,freq" Probably damaging Intolerant radical 10p15.3 isopentenyl-diphosphate delta isomerase 2 1593 rs1044463 SNX2 6643 5 122182555 NM_003100 NP_003091 G/T A384S plus 1513662 1303 SEQUENOM CEPH CEPH (92) 92 0.41 0.23 0.18 276 2 123 by freq Benign 0.218 20 Tolerant 0.78 2.86 24 moderately conservative 605929 5q23 sorting nexin 2 1594 rs1044463 SNX2 6643 5 122182555 NM_003100 NP_003091 G/T A384S plus 24812816 1303 SEQUENOM CEPH CEPH (92) 184 0.14 0.23 0.18 276 2 123 by freq Benign 0.218 20 Tolerant 0.78 2.86 24 moderately conservative 605929 5q23 sorting nexin 2 1595 rs1044498 ENPP1 5167 6 132214061 NM_006208 NP_006199 A/C K121Q plus 12587306 928 IBARROSO ELY UK (Ely region of East Anglia) 921 0.15 0.16 0.02 1061 3 0.13 0.13 92 2 123 "by doubleHit,freq,cluster" Benign 0.943 10 moderately conservative 173335 6q22-q23 ectonucleotide pyrophosphatase/phosphodiesterase 1 1596 rs1044498 ENPP1 5167 6 132214061 NM_006208 NP_006199 A/C K121Q plus 22481659 1303 SEQUENOM CEPH CEPH (92) 92 0.22 0.16 0.02 1061 3 0.13 0.13 92 2 123 "by doubleHit,freq,cluster" Benign 0.943 10 moderately conservative 173335 6q22-q23 ectonucleotide pyrophosphatase/phosphodiesterase 1 1597 rs1044498 ENPP1 5167 6 132214061 NM_006208 NP_006199 A/C K121Q plus 23404875 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.17 0.16 0.02 1061 3 0.13 0.13 92 2 123 "by doubleHit,freq,cluster" Benign 0.943 10 moderately conservative 173335 6q22-q23 ectonucleotide pyrophosphatase/phosphodiesterase 1 1598 rs1045102 CNKSR1 10256 1 26199991 NM_006314 NP_006305 A/T K651M plus 1514971 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 83 0.06 0.06 0 83 1 0.06 0 83 1 86 by freq moderately conservative 603272 1p35.3 connector enhancer of kinase suppressor of Ras 1 1599 rs1045105 CNKSR1 10256 1 26200098 NM_006314 NP_006305 A/C H687N plus 1514976 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 83 0.18 0.11 0.06 295 3 0.28 0.04 166 2 106 "HapMap,submitter,freq" moderately conservative 603272 1p35.3 connector enhancer of kinase suppressor of Ras 1 1600 rs1045105 CNKSR1 10256 1 26200098 NM_006314 NP_006305 A/C H687N plus 1514976 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.08 0.11 0.06 295 3 0.28 0.04 166 2 106 "HapMap,submitter,freq" moderately conservative 603272 1p35.3 connector enhancer of kinase suppressor of Ras 1 1601 rs1045105 CNKSR1 10256 1 26200098 NM_006314 NP_006305 A/C H687N plus 1514976 1303 SEQUENOM CEPH CEPH (92) 92 0.08 0.11 0.06 295 3 0.28 0.04 166 2 106 "HapMap,submitter,freq" moderately conservative 603272 1p35.3 connector enhancer of kinase suppressor of Ras 1 1602 rs1045142 ROCK1 6093 18 16788810 NM_005406 NP_005397 A/G R1262Q minus 3757429 1303 SEQUENOM CEPH CEPH (92) 92 0.02 0.02 0 92 1 106 by freq Possibly damaging 1.583 15 conservative 601702 18q11.2 "Rho-associated, coiled-coil containing protein kinase 1" 1603 rs1045288 PSMD13 5719 11 227087 NM_002817 NP_002808 A/G N13S plus 15814939 1303 SEQUENOM CEPH CEPH (92) 92 0.37 0.37 0 92 1 0.16 0 718 1 121 "by doubleHit,freq,cluster" conservative 603481 11p15.5 "proteasome (prosome, macropain) 26S subunit, non-ATPase, 13" 1604 rs1045332 CGI-105 51011 2 95498556 NM_016044 NP_057128 C/T M198T plus 3270027 1303 SEQUENOM CEPH CEPH (92) 92 0.21 0.21 0 92 1 100 by freq Probably damaging 2.505 8 Tolerant 0.47 2.78 37 moderately conservative 2p24.3-p11.2 CGI-105 protein 1605 rs1045546 TAPBPL 55080 12 6438168 NM_018009 NP_060479 A/G T334M minus 1515844 1303 SEQUENOM CEPH CEPH (92) 92 0.2 0.21 0.02 140 2 0.03 0.01 94 2 123 by freq Tolerant 0.21 2.78 34 moderately conservative 607081 12p13.31 TAP binding protein-like 1606 rs1045546 TAPBPL 55080 12 6438168 NM_018009 NP_060479 A/G T334M minus 24697367 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.23 0.21 0.02 140 2 0.03 0.01 94 2 123 by freq Tolerant 0.21 2.78 34 moderately conservative 607081 12p13.31 TAP binding protein-like 1607 rs1045922 RNASE6 6039 14 20319964 NM_005615 NP_005606 A/G R89Q plus 1516639 1303 SEQUENOM CEPH CEPH (92) 46 0.5 0.5 0 46 1 123 by freq conservative 601981 14q11.2 "ribonuclease, RNase A family, k6" 1608 rs1046088 EP300 2033 22 39898883 NM_001429 NP_001420 A/C Q2223P plus 13361762 1303 SEQUENOM CEPH CEPH (92) 92 0.2 0.2 0 92 1 119 by freq moderately conservative 602700 22q13.2 E1A binding protein p300 1609 rs1046097 TUBG2 27175 17 38072225 NM_016437 NP_057521 A/G M413V plus 10856512 1303 SEQUENOM CEPH CEPH (92) 92 0.41 0.41 0 92 1 0.47 0 1500 1 121 "by doubleHit,freq,cluster" Borderline 1.151 60 conservative 605785 17q21 "tubulin, gamma 2" 1610 rs1046116 PKP2 5318 12 32913201 NM_004572 NP_004563 C/T L366P minus 12223634 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.24 0.18 0.09 212 2 120 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 602861 12p11 plakophilin 2 1611 rs1046116 PKP2 5318 12 32913201 NM_004572 NP_004563 C/T L366P minus 12223634 1303 SEQUENOM CEPH CEPH (92) 92 0.11 0.18 0.09 212 2 120 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 602861 12p11 plakophilin 2 1612 rs1046248 BDKRB2 624 14 95773237 NM_000623 NP_000614 C/T R14C plus 1517248 1303 SEQUENOM CEPH CEPH (92) 92 0.17 0.15 0.03 370 4 0.07 0 90 2 123 by freq radical 113503 14q32.1-q32.2 bradykinin receptor B2 1613 rs1046248 BDKRB2 624 14 95773237 NM_000623 NP_000614 C/T R14C plus 2981655 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.17 0.15 0.03 370 4 0.07 0 90 2 123 by freq radical 113503 14q32.1-q32.2 bradykinin receptor B2 1614 rs1046248 BDKRB2 624 14 95773237 NM_000623 NP_000614 C/T R14C plus 24607243 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.17 0.15 0.03 370 4 0.07 0 90 2 123 by freq radical 113503 14q32.1-q32.2 bradykinin receptor B2 1615 rs1046248 BDKRB2 624 14 95773237 NM_000623 NP_000614 C/T R14C plus 24795976 1303 SEQUENOM CEPH CEPH (92) 184 0.12 0.15 0.03 370 4 0.07 0 90 2 123 by freq radical 113503 14q32.1-q32.2 bradykinin receptor B2 1616 rs1046268 TJP3 27134 19 3701615 NM_014428 NP_055243 C/T M931T plus 12469289 1303 SEQUENOM CEPH CEPH (92) 92 0.49 0.49 0 92 1 120 "by doubleHit,freq,cluster" Possibly damaging 1.711 5 moderately conservative 19p13.3 tight junction protein 3 (zona occludens 3) 1617 rs1046658 RECK 8434 9 36073430 NM_021111 NP_066934 C/T R170X plus 1518040 1303 SEQUENOM CEPH CEPH (92) 92 0.08 0.08 0 92 1 106 by freq Probably damaging Intolerant radical 605227 9p13-p12 reversion-inducing-cysteine-rich protein with kazal motifs 1618 rs1046668 TNFAIP6 7130 2 152052078 NM_007115 NP_009046 A/G Q144R plus 3296528 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.13 0.16 0.08 258 3 0.21 0.09 94 2 123 "HapMap,doubleHit,freq,cluster" Tolerant 0.45 2.98 121 conservative 600410 2q24.1 "tumor necrosis factor, alpha-induced protein 6" 1619 rs1046668 TNFAIP6 7130 2 152052078 NM_007115 NP_009046 A/G Q144R plus 3296528 1303 SEQUENOM CEPH CEPH (92) 92 0.25 0.16 0.08 258 3 0.21 0.09 94 2 123 "HapMap,doubleHit,freq,cluster" Tolerant 0.45 2.98 121 conservative 600410 2q24.1 "tumor necrosis factor, alpha-induced protein 6" 1620 rs1046668 TNFAIP6 7130 2 152052078 NM_007115 NP_009046 A/G Q144R plus 23253087 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.16 0.08 258 3 0.21 0.09 94 2 123 "HapMap,doubleHit,freq,cluster" Tolerant 0.45 2.98 121 conservative 600410 2q24.1 "tumor necrosis factor, alpha-induced protein 6" 1621 rs1046974 SAG 6295 2 234037547 NM_000541 NP_000532 A/G V403I plus 16874051 1303 SEQUENOM CEPH CEPH (92) 92 0.34 0.34 0 92 1 120 "by doubleHit,submitter,freq,cluster" conservative 181031 2q37.1 S-antigen; retina and pineal gland (arrestin) 1622 rs1046984 BRCA2 675 13 31805411 NM_000059 NP_000050 C/T S599F plus 1518650 1303 SEQUENOM CEPH CEPH (92) 92 0.14 0.14 0 92 1 86 by freq Probably damaging 1.998 9 radical 600185 13q12.3 "breast cancer 2, early onset" 1623 rs1047286 C3 718 19 6664262 NM_000064 NP_000055 C/T P314L minus 3177315 619 WICVAR MITOGPOP6 CORIELL Mixed 52 0.19 0.19 0 52 1 102 by freq Possibly damaging 1.514 9 moderately conservative 120700 19p13.3-p13.2 complement component 3 1624 rs1047303 HSD3B1 3283 1 119769288 NM_000862 NP_000853 A/C T367N plus 6413600 1303 SEQUENOM CEPH CEPH (92) 92 0.48 0.48 0 92 1 0.06 0 1378 1 121 "by doubleHit,freq,cluster" Possibly damaging 1.503 29 Tolerant 0.3 3.19 29 moderately conservative 109715 1p13.1 "hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1" 1625 rs1047325 S100A2 6273 1 150347100 NM_005978 NP_005969 A/G S61N minus 15433527 1303 SEQUENOM CEPH CEPH (92) 92 0.16 0.13 0.05 140 2 0.21 0.28 90 2 123 "by cluster,freq" Potentially damaging 1.279 7 Tolerant 0.33 2.79 44 conservative 176993 1q21 S100 calcium binding protein A2 1626 rs1047325 S100A2 6273 1 150347100 NM_005978 NP_005969 A/G S61N minus 23213597 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.13 0.05 140 2 0.21 0.28 90 2 123 "by cluster,freq" Potentially damaging 1.279 7 Tolerant 0.33 2.79 44 conservative 176993 1q21 S100 calcium binding protein A2 1627 rs1047372 PCDHB2 56133 5 140456837 NM_018936 NP_061759 A/G G760D plus 24815868 1303 SEQUENOM CEPH CEPH (92) 184 0.38 0.38 0 184 1 123 "by cluster,freq" Benign 0.231 98 Tolerant 1 2.77 127 moderately conservative 606328 5q31 protocadherin beta 2 1628 rs1047626 SLC30A9 10463 4 41844599 NM_006345 NP_006336 A/G M50V plus 24655325 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.38 0.38 0 48 1 0.16 0.14 94 2 123 "by doubleHit,freq,cluster" Benign 0.86 5 conservative 604604 4p13-p12 "solute carrier family 30 (zinc transporter), member 9" 1629 rs1047640 SP3 6670 2 174646257 NM_003111 NP_003102 A/G T164A minus 16844292 1303 SEQUENOM CEPH CEPH (92) 92 0.16 0.16 0 92 1 0.32 0 1492 1 121 "by doubleHit,freq,cluster" Tolerant 1 3.04 23 moderately conservative 601804 2q31 Sp3 transcription factor 1630 rs1047769 ERCC5 2073 13 102311945 NM_000123 NP_000114 A/G M254V plus 5605242 693 EGP_SNPS PDR90 NIHPDR 178 0.03 0.03 0.01 330 3 0.04 0.02 240 2 118 "by cluster,freq" Possibly damaging 1.528 7 Tolerant 0.25 2.9 8 conservative 133530 13q22 "excision repair cross-complementing rodent repair deficiency, complementation group 5 (xeroderma pigmentosum, complementation group G (Cockayne syndrome))" 1631 rs1047769 ERCC5 2073 13 102311945 NM_000123 NP_000114 A/G M254V plus 5605242 1303 SEQUENOM CEPH CEPH (92) 92 0.02 0.03 0.01 330 3 0.04 0.02 240 2 118 "by cluster,freq" Possibly damaging 1.528 7 Tolerant 0.25 2.9 8 conservative 133530 13q22 "excision repair cross-complementing rodent repair deficiency, complementation group 5 (xeroderma pigmentosum, complementation group G (Cockayne syndrome))" 1632 rs1047769 ERCC5 2073 13 102311945 NM_000123 NP_000114 A/G M254V plus 12675394 775 SNP500CANCER CAUC1 Caucasian (31) 60 0.05 0.03 0.01 330 3 0.04 0.02 240 2 118 "by cluster,freq" Possibly damaging 1.528 7 Tolerant 0.25 2.9 8 conservative 133530 13q22 "excision repair cross-complementing rodent repair deficiency, complementation group 5 (xeroderma pigmentosum, complementation group G (Cockayne syndrome))" 1633 rs1047855 ENTPD3 956 3 40443900 NM_001248 NP_001239 C/T A496V plus 16972678 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.27 0.27 0 120 1 120 "HapMap,freq,cluster" moderately conservative 603161 3p21.3 ectonucleoside triphosphate diphosphohydrolase 3 1634 rs1047991 PAPD1 55149 10 30669232 NM_018109 NP_060579 A/G R162C plus 20687231 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.35 0.39 0.08 260 3 0.2 0.07 94 2 123 "HapMap,doubleHit,freq" Possibly damaging 1.744 5 Intolerant 0.03 2.94 16 radical 10p12.1 PAP associated domain containing 1 1635 rs1047991 PAPD1 55149 10 30669232 NM_018109 NP_060579 A/G R162C plus 20687231 1303 SEQUENOM CEPH CEPH (92) 92 0.47 0.39 0.08 260 3 0.2 0.07 94 2 123 "HapMap,doubleHit,freq" Possibly damaging 1.744 5 Intolerant 0.03 2.94 16 radical 10p12.1 PAP associated domain containing 1 1636 rs1047991 PAPD1 55149 10 30669232 NM_018109 NP_060579 A/G R162C plus 24624214 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.31 0.39 0.08 260 3 0.2 0.07 94 2 123 "HapMap,doubleHit,freq" Possibly damaging 1.744 5 Intolerant 0.03 2.94 16 radical 10p12.1 PAP associated domain containing 1 1637 rs1048108 BARD1 580 2 215499730 NM_000465 NP_000456 C/T P24S minus 1520704 1303 SEQUENOM CEPH CEPH (92) 92 0.42 0.41 0.03 140 2 0.33 0.13 94 2 123 "by cluster,freq" moderately conservative 601593 2q34-q35 BRCA1 associated RING domain 1 1638 rs1048108 BARD1 580 2 215499730 NM_000465 NP_000456 C/T P24S minus 23927969 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.38 0.41 0.03 140 2 0.33 0.13 94 2 123 "by cluster,freq" moderately conservative 601593 2q34-q35 BRCA1 associated RING domain 1 1639 rs1048135 NMI 9111 2 151964924 NM_004688 NP_004679 C/T S16L minus 21598065 1303 SEQUENOM CEPH CEPH (92) 92 0.46 0.43 0.05 140 2 0.2 0.17 92 2 123 by freq moderately radical 603525 2p24.3-q21.3 N-myc (and STAT) interactor 1640 rs1048135 NMI 9111 2 151964924 NM_004688 NP_004679 C/T S16L minus 24309331 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.38 0.43 0.05 140 2 0.2 0.17 92 2 123 by freq moderately radical 603525 2p24.3-q21.3 N-myc (and STAT) interactor 1641 rs1048197 SMPD2 6610 6 109869025 NM_003080 NP_003071 A/G P3L minus 1520899 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.04 0.03 0.02 212 2 123 "HapMap,submitter,freq" moderately conservative 603498 6q21 "sphingomyelin phosphodiesterase 2, neutral membrane (neutral sphingomyelinase)" 1642 rs1048197 SMPD2 6610 6 109869025 NM_003080 NP_003071 A/G P3L minus 1520899 1303 SEQUENOM CEPH CEPH (92) 92 0.01 0.03 0.02 212 2 123 "HapMap,submitter,freq" moderately conservative 603498 6q21 "sphingomyelin phosphodiesterase 2, neutral membrane (neutral sphingomyelinase)" 1643 rs1048430 HLA-DQA1 3117 6 32718465 NM_002122 NP_002113 C/G F238L plus 24816176 1303 SEQUENOM CEPH CEPH (92) 184 0.43 0.43 0 184 1 123 by freq Benign 0.414 162 Tolerant 1 2.84 257 conservative 146880 6p21.3 "major histocompatibility complex, class II, DQ alpha 1" 1644 rs1048661 LOXL1 4016 15 72006599 NM_005576 NP_005567 G/T R141L plus 4929216 1303 SEQUENOM CEPH CEPH (92) 92 0.04 0.04 0 92 1 0.44 0 1496 1 108 "by cluster,freq" moderately radical 153456 15q22 lysyl oxidase-like 1 1645 rs1048889 DDX54 79039 12 112059586 NM_024072 NP_076977 C/T P822L minus 1522193 1303 SEQUENOM CEPH CEPH (92) 92 0.39 0.39 0 92 1 123 by freq Benign 0.225 7 moderately conservative 12q24.21 DEAD (Asp-Glu-Ala-Asp) box polypeptide 54 1646 rs1048943 CYP1A1 1543 15 72800038 NM_000499 NP_000490 A/G I462V minus 3176140 619 WICVAR MITOGPOP6 CORIELL Mixed 60 0.02 0.07 0.07 118 2 0.17 0.07 370 4 116 "by cluster,freq" Benign 0.906 90 Borderline 0.11 2.81 88 conservative 108330 15q22-q24 "cytochrome P450, family 1, subfamily A, polypeptide 1" 1647 rs1048943 CYP1A1 1543 15 72800038 NM_000499 NP_000490 A/G I462V minus 5586386 775 SNP500CANCER CAUC1 Caucasian (31) 58 0.12 0.07 0.07 118 2 0.17 0.07 370 4 116 "by cluster,freq" Benign 0.906 90 Borderline 0.11 2.81 88 conservative 108330 15q22-q24 "cytochrome P450, family 1, subfamily A, polypeptide 1" 1648 rs1049125 PNLIPRP1 5407 10 118358596 NM_006229 NP_006220 C/T L461P plus 19174353 1303 SEQUENOM CEPH CEPH (92) 92 0.12 0.12 0.01 140 2 0.07 0.04 94 2 123 "by cluster,freq" Probably damaging 2.033 40 Intolerant 0.01 3.09 28 moderately conservative 604422 10q26.12 pancreatic lipase-related protein 1 1649 rs1049125 PNLIPRP1 5407 10 118358596 NM_006229 NP_006220 C/T L461P plus 24600233 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.12 0.01 140 2 0.07 0.04 94 2 123 "by cluster,freq" Probably damaging 2.033 40 Intolerant 0.01 3.09 28 moderately conservative 604422 10q26.12 pancreatic lipase-related protein 1 1650 rs1049254 CYBA 1535 16 87237329 NM_000101 NP_000092 C/T V174A minus 24694530 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.48 0.48 0 46 1 0.25 0.1 84 2 123 "by doubleHit,freq,cluster" Benign 0.116 9 moderately conservative 608508 16q24 "cytochrome b-245, alpha polypeptide" 1651 rs1049296 TF 7018 3 134977052 NM_001063 NP_001054 C/T P589S plus 8820437 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.04 0.09 0.05 138 2 0.07 0 46 1 120 "by cluster,freq" Borderline 1.244 83 Borderline 0.11 2.82 93 moderately conservative 190000 3q22.1 transferrin 1652 rs1049296 TF 7018 3 134977052 NM_001063 NP_001054 C/T P589S plus 8820437 1303 SEQUENOM CEPH CEPH (92) 92 0.12 0.09 0.05 138 2 0.07 0 46 1 120 "by cluster,freq" Borderline 1.244 83 Borderline 0.11 2.82 93 moderately conservative 190000 3q22.1 transferrin 1653 rs1049306 PDHX 8050 11 34894845 NM_003477 NP_003468 C/T R23C plus 12148948 1303 SEQUENOM CEPH CEPH (92) 92 0.36 0.17 0.12 460 3 123 "by doubleHit,freq,cluster" radical 608769 11p13 "pyruvate dehydrogenase complex, component X" 1654 rs1049306 PDHX 8050 11 34894845 NM_003477 NP_003468 C/T R23C plus 24797023 1303 SEQUENOM CEPH CEPH (92) 184 0.12 0.17 0.12 460 3 123 "by doubleHit,freq,cluster" radical 608769 11p13 "pyruvate dehydrogenase complex, component X" 1655 rs1049306 PDHX 8050 11 34894845 NM_003477 NP_003468 C/T R23C plus 24816514 1303 SEQUENOM CEPH CEPH (92) 184 0.12 0.17 0.12 460 3 123 "by doubleHit,freq,cluster" radical 608769 11p13 "pyruvate dehydrogenase complex, component X" 1656 rs1049544 SPARCL1 8404 4 88772815 NM_004684 NP_004675 C/G H106D minus 4949430 1303 SEQUENOM CEPH CEPH (92) 92 0.33 0.35 0.05 140 2 0.37 0.11 88 2 123 "by doubleHit,freq,cluster" Possibly damaging 1.575 5 moderately conservative 606041 4q22.1 "SPARC-like 1 (mast9, hevin)" 1657 rs1049544 SPARCL1 8404 4 88772815 NM_004684 NP_004675 C/G H106D minus 23881462 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.4 0.35 0.05 140 2 0.37 0.11 88 2 123 "by doubleHit,freq,cluster" Possibly damaging 1.575 5 moderately conservative 606041 4q22.1 "SPARC-like 1 (mast9, hevin)" 1658 rs1049564 NP 4860 14 20010446 NM_000270 NP_000261 C/T G51S minus 23617308 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.15 0 48 1 0.27 0.2 94 2 123 "by doubleHit,freq,cluster" Potentially damaging 1.411 31 moderately conservative 164050 14q13.1 nucleoside phosphorylase 1659 rs1049742 ABP1 26 7 149992201 NM_001091 NP_001082 C/T S332F plus 17939745 1303 SEQUENOM CEPH CEPH (92) 92 0.09 0.09 0 92 1 121 "by doubleHit,freq,cluster" Possibly damaging 1.954 11 Intolerant 0 2.76 26 radical 104610 7q34-q36 amiloride binding protein 1 (amine oxidase (copper-containing)) 1660 rs1049925 PHC1 1911 12 8978165 NM_004426 NP_004417 C/T T693A minus 24698787 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.46 0.26 0.14 232 2 0.24 0.16 94 2 123 "by doubleHit,submitter,freq,cluster" Benign 0.222 12 Tolerant 1 3.03 23 moderately conservative 602978 12p13 polyhomeotic-like 1 (Drosophila) 1661 rs1049925 PHC1 1911 12 8978165 NM_004426 NP_004417 C/T T693A minus 24796441 1303 SEQUENOM CEPH CEPH (92) 184 0.21 0.26 0.14 232 2 0.24 0.16 94 2 123 "by doubleHit,submitter,freq,cluster" Benign 0.222 12 Tolerant 1 3.03 23 moderately conservative 602978 12p13 polyhomeotic-like 1 (Drosophila) 1662 rs1049970 CDH5 1003 16 64989924 NM_001795 NP_001786 C/T I517T plus 14254569 1303 SEQUENOM CEPH CEPH (92) 92 0.39 0.39 0 92 1 120 "by doubleHit,freq,cluster" Benign 0.675 7 moderately conservative 601120 16q22.1 "cadherin 5, type 2, VE-cadherin (vascular epithelium)" 1663 rs1050110 ADPRTL1 143 13 23907485 NM_006437 NP_006428 C/G G1265A minus 5586211 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.47 0.44 0.11 190 4 0.31 0.07 1710 8 116 "by doubleHit,freq,cluster" moderately conservative 607519 13q11 ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1 1664 rs1050110 ADPRTL1 143 13 23907485 NM_006437 NP_006428 C/G G1265A minus 5586211 902 AFFY Caucasian 24 0.25 0.44 0.11 190 4 0.31 0.07 1710 8 116 "by doubleHit,freq,cluster" moderately conservative 607519 13q11 ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1 1665 rs1050110 ADPRTL1 143 13 23907485 NM_006437 NP_006428 C/G G1265A minus 5586211 904 AFFY CEPH 12 0.25 0.44 0.11 190 4 0.31 0.07 1710 8 116 "by doubleHit,freq,cluster" moderately conservative 607519 13q11 ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1 1666 rs1050110 ADPRTL1 143 13 23907485 NM_006437 NP_006428 C/G G1265A minus 5586211 1303 SEQUENOM CEPH CEPH (92) 92 0.49 0.44 0.11 190 4 0.31 0.07 1710 8 116 "by doubleHit,freq,cluster" moderately conservative 607519 13q11 ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1 1667 rs1050112 ADPRTL1 143 13 23907297 NM_006437 NP_006428 A/C P1328T minus 5586216 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.47 0.48 0.02 108 2 0.32 0.07 1838 5 120 "by doubleHit,freq,cluster" conservative 607519 13q11 ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1 1668 rs1050112 ADPRTL1 143 13 23907297 NM_006437 NP_006428 A/C P1328T minus 5586216 1303 SEQUENOM CEPH CEPH (92) 46 0.5 0.48 0.02 108 2 0.32 0.07 1838 5 120 "by doubleHit,freq,cluster" conservative 607519 13q11 ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1 1669 rs1050114 ADPRTL1 143 13 23907288 NM_006437 NP_006428 A/G A1331T minus 5586217 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.02 0.04 0.03 154 2 0.08 0.05 298 3 113 "by cluster,freq" moderately conservative 607519 13q11 ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1 1670 rs1050114 ADPRTL1 143 13 23907288 NM_006437 NP_006428 A/G A1331T minus 5586217 1303 SEQUENOM CEPH CEPH (92) 92 0.06 0.04 0.03 154 2 0.08 0.05 298 3 113 "by cluster,freq" moderately conservative 607519 13q11 ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1 1671 rs1050152 SLC22A4 6583 5 131704219 NM_003059 NP_003050 C/T L503F plus 24379843 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.42 0.42 0 48 1 0.18 0.06 596 2 123 "by cluster,freq" Benign 0.132 12 Potentially intolerant 0.06 2.81 21 conservative 604190 5q31.1 "solute carrier family 22 (organic cation transporter), member 4" 1672 rs1050160 GLUD1 2746 10 88844232 NM_005271 NP_005262 A/G R92Q minus 24797030 1303 SEQUENOM CEPH CEPH (92) 184 0.28 0.28 0 184 1 123 by freq Potentially damaging 1.247 32 Tolerant 0.7 3.07 55 conservative 138130 10q23.3 glutamate dehydrogenase 1 1673 rs1050348 LAMA4 3910 6 112600565 NM_002290 NP_002281 C/T Y491H minus 3156356 1303 SEQUENOM CEPH CEPH (92) 92 0.38 0.37 0.02 140 2 0.22 0.02 94 2 123 "by doubleHit,freq,cluster" Possibly damaging 1.711 6 moderately conservative 600133 6q21 "laminin, alpha 4" 1674 rs1050348 LAMA4 3910 6 112600565 NM_002290 NP_002281 C/T Y491H minus 24413213 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.35 0.37 0.02 140 2 0.22 0.02 94 2 123 "by doubleHit,freq,cluster" Possibly damaging 1.711 6 moderately conservative 600133 6q21 "laminin, alpha 4" 1675 rs1050349 LAMA4 3910 6 112564076 NM_002290 NP_002281 C/G P1112R minus 2941526 1303 SEQUENOM CEPH CEPH (92) 92 0.15 0.15 0 92 1 116 "by doubleHit,submitter,cluster" Benign 0.521 8 moderately radical 600133 6q21 "laminin, alpha 4" 1676 rs1050354 PPIG 9360 2 170318610 NM_004792 NP_004783 A/T D445E plus 11496510 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.48 0.44 0.05 260 3 0.33 0.1 90 2 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 0.77 3.02 8 conservative 606093 2q31.1 peptidyl-prolyl isomerase G (cyclophilin G) 1677 rs1050354 PPIG 9360 2 170318610 NM_004792 NP_004783 A/T D445E plus 11496510 1303 SEQUENOM CEPH CEPH (92) 92 0.41 0.44 0.05 260 3 0.33 0.1 90 2 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 0.77 3.02 8 conservative 606093 2q31.1 peptidyl-prolyl isomerase G (cyclophilin G) 1678 rs1050354 PPIG 9360 2 170318610 NM_004792 NP_004783 A/T D445E plus 24369174 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.4 0.44 0.05 260 3 0.33 0.1 90 2 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 0.77 3.02 8 conservative 606093 2q31.1 peptidyl-prolyl isomerase G (cyclophilin G) 1679 rs1050450 GPX1 2876 3 49369838 NM_000581 NP_000572 C/T P200L minus 5586547 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.19 0.15 0.03 424 3 0.16 0.06 346 4 123 "by doubleHit,freq,cluster" Benign 0.486 12 Borderline 0.12 3.16 23 moderately conservative 138320 3p21.3 glutathione peroxidase 1 1680 rs1050450 GPX1 2876 3 49369838 NM_000581 NP_000572 C/T P200L minus 12568572 693 EGP_SNPS PDR90 NIHPDR 178 0.17 0.15 0.03 424 3 0.16 0.06 346 4 123 "by doubleHit,freq,cluster" Benign 0.486 12 Borderline 0.12 3.16 23 moderately conservative 138320 3p21.3 glutathione peroxidase 1 1681 rs1050450 GPX1 2876 3 49369838 NM_000581 NP_000572 C/T P200L minus 24787925 1303 SEQUENOM CEPH CEPH (92) 184 0.12 0.15 0.03 424 3 0.16 0.06 346 4 123 "by doubleHit,freq,cluster" Benign 0.486 12 Borderline 0.12 3.16 23 moderately conservative 138320 3p21.3 glutathione peroxidase 1 1682 rs1050501 FCGR2B 2213 1 158375465 NM_004001 NP_003992 C/T I225T plus 19838944 1303 SEQUENOM CEPH CEPH (92) 92 0.11 0.12 0.03 140 2 0.28 0.02 94 2 123 "by doubleHit,freq,cluster" Benign 0.237 40 Tolerant 0.22 2.75 39 moderately conservative 604590 1q23 "Fc fragment of IgG, low affinity IIb, receptor for (CD32)" 1683 rs1050501 FCGR2B 2213 1 158375465 NM_004001 NP_003992 C/T I225T plus 23842385 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.12 0.03 140 2 0.28 0.02 94 2 123 "by doubleHit,freq,cluster" Benign 0.237 40 Tolerant 0.22 2.75 39 moderately conservative 604590 1q23 "Fc fragment of IgG, low affinity IIb, receptor for (CD32)" 1684 rs1050565 BLMH 642 17 25600202 NM_000386 NP_000377 A/G I443V minus 3217070 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.3 0.3 0.04 258 3 0.18 0.03 1596 3 123 "HapMap,freq,cluster" Benign 0.986 12 Tolerant 1 2.82 33 conservative 602403 17q11.2 bleomycin hydrolase 1685 rs1050565 BLMH 642 17 25600202 NM_000386 NP_000377 A/G I443V minus 3217070 1303 SEQUENOM CEPH CEPH (92) 92 0.26 0.3 0.04 258 3 0.18 0.03 1596 3 123 "HapMap,freq,cluster" Benign 0.986 12 Tolerant 1 2.82 33 conservative 602403 17q11.2 bleomycin hydrolase 1686 rs1050565 BLMH 642 17 25600202 NM_000386 NP_000377 A/G I443V minus 24705757 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.35 0.3 0.04 258 3 0.18 0.03 1596 3 123 "HapMap,freq,cluster" Benign 0.986 12 Tolerant 1 2.82 33 conservative 602403 17q11.2 bleomycin hydrolase 1687 rs1050767 MKI67 4288 10 129791936 NM_002417 NP_002408 A/C T2720P minus 14315599 1303 SEQUENOM CEPH CEPH (92) 92 0.16 0.16 0 92 1 121 "by doubleHit,freq,cluster" Tolerant 0.23 2.84 10 conservative 176741 10q25-qter antigen identified by monoclonal antibody Ki-67 1688 rs1050916 BLVRA 644 7 43604120 NM_000712 NP_000703 A/G Q56R plus 1525956 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.03 0.03 0 118 1 106 "HapMap,freq" Potentially damaging 1.432 7 Tolerant 0.51 2.75 15 conservative 109750 7p14-cen biliverdin reductase A 1689 rs1050998 CXCL16 58191 17 4585486 NM_022059 NP_071342 C/T I142T minus 12391137 1303 SEQUENOM CEPH CEPH (92) 92 0.28 0.3 0.05 140 2 0.41 0.03 1588 3 123 "by doubleHit,freq,cluster" moderately conservative 605398 17p13 chemokine (C-X-C motif) ligand 16 1690 rs1050998 CXCL16 58191 17 4585486 NM_022059 NP_071342 C/T I142T minus 24213400 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.35 0.3 0.05 140 2 0.41 0.03 1588 3 123 "by doubleHit,freq,cluster" moderately conservative 605398 17p13 chemokine (C-X-C motif) ligand 16 1691 rs1051042 OAS1 4938 12 111819957 NM_016816 NP_058132 C/G R361T plus 16591428 1303 SEQUENOM CEPH CEPH (92) 92 0.24 0.3 0.13 138 2 0.17 0.08 94 2 123 "by doubleHit,freq,cluster" moderately conservative 164350 12q24.1 "2',5'-oligoadenylate synthetase 1, 40/46kDa" 1692 rs1051042 OAS1 4938 12 111819957 NM_016816 NP_058132 C/G R361T plus 24415249 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.43 0.3 0.13 138 2 0.17 0.08 94 2 123 "by doubleHit,freq,cluster" moderately conservative 164350 12q24.1 "2',5'-oligoadenylate synthetase 1, 40/46kDa" 1693 rs1051061 VRK2 7444 2 58228465 NM_006296 NP_006287 A/G I167V plus 4474748 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.34 0.33 0.01 260 3 0.42 0.07 1584 3 123 "HapMap,submitter,freq,cluster" Benign 0.3 8 conservative 602169 2p16-p15 vaccinia related kinase 2 1694 rs1051061 VRK2 7444 2 58228465 NM_006296 NP_006287 A/G I167V plus 4474748 1303 SEQUENOM CEPH CEPH (92) 92 0.32 0.33 0.01 260 3 0.42 0.07 1584 3 123 "HapMap,submitter,freq,cluster" Benign 0.3 8 conservative 602169 2p16-p15 vaccinia related kinase 2 1695 rs1051061 VRK2 7444 2 58228465 NM_006296 NP_006287 A/G I167V plus 23899502 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.31 0.33 0.01 260 3 0.42 0.07 1584 3 123 "HapMap,submitter,freq,cluster" Benign 0.3 8 conservative 602169 2p16-p15 vaccinia related kinase 2 1696 rs1051130 CCND3 896 6 42011760 NM_001760 NP_001751 G/T S259A minus 3177789 619 WICVAR MITOGPOP6 CORIELL Mixed 26 0.23 0.33 0.05 288 3 0.46 0 1290 1 121 "by doubleHit,freq,cluster" Benign 0.162 26 Tolerant 0.4 3.13 29 moderately conservative 123834 6p21 cyclin D3 1697 rs1051130 CCND3 896 6 42011760 NM_001760 NP_001751 G/T S259A minus 4479170 693 EGP_SNPS PDR90 NIHPDR 170 0.36 0.33 0.05 288 3 0.46 0 1290 1 121 "by doubleHit,freq,cluster" Benign 0.162 26 Tolerant 0.4 3.13 29 moderately conservative 123834 6p21 cyclin D3 1698 rs1051130 CCND3 896 6 42011760 NM_001760 NP_001751 G/T S259A minus 4479170 1303 SEQUENOM CEPH CEPH (92) 92 0.3 0.33 0.05 288 3 0.46 0 1290 1 121 "by doubleHit,freq,cluster" Benign 0.162 26 Tolerant 0.4 3.13 29 moderately conservative 123834 6p21 cyclin D3 1699 rs1051193 SEL1L 6400 14 81015744 NM_005065 NP_005056 A/G V714I minus 1526538 1303 SEQUENOM CEPH CEPH (92) 92 0.03 0.03 0 92 1 86 by freq Benign 0.225 6 Tolerant 0.57 2.85 25 conservative 602329 14q24.3-q31 sel-1 suppressor of lin-12-like (C. elegans) 1700 rs1051266 SLC19A1 6573 21 45782222 NM_194255 NP_919231 A/G H27R minus 3177864 619 WICVAR MITOGPOP6 CORIELL Mixed 54 0.13 0.26 0.14 146 2 0.44 0 598 1 121 "by doubleHit,freq,cluster" Tolerant 0.35 2.83 35 conservative 600424 21q22.3 "solute carrier family 19 (folate transporter), member 1" 1701 rs1051266 SLC19A1 6573 21 45782222 NM_194255 NP_919231 A/G H27R minus 21819753 1303 SEQUENOM CEPH CEPH (92) 92 0.33 0.26 0.14 146 2 0.44 0 598 1 121 "by doubleHit,freq,cluster" Tolerant 0.35 2.83 35 conservative 600424 21q22.3 "solute carrier family 19 (folate transporter), member 1" 1702 rs1051309 ANKHD1 54882 5 139886028 NM_017747 NP_060217 A/G G1586S plus 1526754 1303 SEQUENOM CEPH CEPH (92) 92 0.03 0.03 0 92 1 106 by freq moderately conservative 5q31.3 ankyrin repeat and KH domain containing 1 1703 rs1051338 LIPA 3988 10 90997340 NM_000235 NP_000226 A/C T16P minus 3176256 619 WICVAR MITOGPOP6 CORIELL Mixed 46 0.3 0.3 0.05 300 4 0.21 0.16 86 2 123 "HapMap,submitter,freq,cluster" Benign 0.45 7 Tolerant 0.21 2.98 24 conservative 278000 10q23.2-q23.3 "lipase A, lysosomal acid, cholesterol esterase (Wolman disease)" 1704 rs1051338 LIPA 3988 10 90997340 NM_000235 NP_000226 A/C T16P minus 3500320 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.33 0.3 0.05 300 4 0.21 0.16 86 2 123 "HapMap,submitter,freq,cluster" Benign 0.45 7 Tolerant 0.21 2.98 24 conservative 278000 10q23.2-q23.3 "lipase A, lysosomal acid, cholesterol esterase (Wolman disease)" 1705 rs1051338 LIPA 3988 10 90997340 NM_000235 NP_000226 A/C T16P minus 3500320 1303 SEQUENOM CEPH CEPH (92) 92 0.31 0.3 0.05 300 4 0.21 0.16 86 2 123 "HapMap,submitter,freq,cluster" Benign 0.45 7 Tolerant 0.21 2.98 24 conservative 278000 10q23.2-q23.3 "lipase A, lysosomal acid, cholesterol esterase (Wolman disease)" 1706 rs1051338 LIPA 3988 10 90997340 NM_000235 NP_000226 A/C T16P minus 24085876 1371 PERLEGEN AFD_EUR_PANEL European American (24) 42 0.19 0.3 0.05 300 4 0.21 0.16 86 2 123 "HapMap,submitter,freq,cluster" Benign 0.45 7 Tolerant 0.21 2.98 24 conservative 278000 10q23.2-q23.3 "lipase A, lysosomal acid, cholesterol esterase (Wolman disease)" 1707 rs1051484 PREP 5550 6 105832729 NM_002726 NP_002717 C/T V706I plus 1673280 1303 SEQUENOM CEPH CEPH (92) 92 0.29 0.16 0.11 242 4 0.3 0.04 1618 5 123 "by doubleHit,freq,cluster" Benign 0.337 16 Tolerant 0.88 2.94 21 conservative 600400 6q22 prolyl endopeptidase 1708 rs1051484 PREP 5550 6 105832729 NM_002726 NP_002717 C/T V706I plus 2588301 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.07 0.16 0.11 242 4 0.3 0.04 1618 5 123 "by doubleHit,freq,cluster" Benign 0.337 16 Tolerant 0.88 2.94 21 conservative 600400 6q22 prolyl endopeptidase 1709 rs1051484 PREP 5550 6 105832729 NM_002726 NP_002717 C/T V706I plus 2588301 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 90 0.09 0.16 0.11 242 4 0.3 0.04 1618 5 123 "by doubleHit,freq,cluster" Benign 0.337 16 Tolerant 0.88 2.94 21 conservative 600400 6q22 prolyl endopeptidase 1710 rs1051484 PREP 5550 6 105832729 NM_002726 NP_002717 C/T V706I plus 23495927 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.09 0.16 0.11 242 4 0.3 0.04 1618 5 123 "by doubleHit,freq,cluster" Benign 0.337 16 Tolerant 0.88 2.94 21 conservative 600400 6q22 prolyl endopeptidase 1711 rs1051489 ZFR 51663 5 32436023 NM_016107 NP_057191 C/T I520T minus 3249658 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.29 0.26 0.04 212 2 121 "HapMap,submitter,freq,cluster" Benign 0.066 7 moderately conservative 5p13.3 zinc finger RNA binding protein 1712 rs1051489 ZFR 51663 5 32436023 NM_016107 NP_057191 C/T I520T minus 22301778 1303 SEQUENOM CEPH CEPH (92) 92 0.23 0.26 0.04 212 2 121 "HapMap,submitter,freq,cluster" Benign 0.066 7 moderately conservative 5p13.3 zinc finger RNA binding protein 1713 rs1051505 ARID3A 1820 19 922949 NM_005224 NP_005215 A/G G556S plus 12474446 1303 SEQUENOM CEPH CEPH (92) 92 0.13 0.13 0 92 1 121 "by doubleHit,freq,cluster" moderately conservative 603265 19p13.3 AT rich interactive domain 3A (BRIGHT- like) 1714 rs1051566 GSTA1 2938 6 52771991 NM_145740 NP_665683 A/G A12T minus 1527223 1303 SEQUENOM CEPH CEPH (92) 92 0.28 0.28 0 92 1 106 by freq Benign 0.009 57 Tolerant 0.34 2.85 64 moderately conservative 138359 6p12.1 glutathione S-transferase A1 1715 rs1051578 GSTA1 2938 6 52771969 NM_145740 NP_665683 C/T T19I minus 1527259 1303 SEQUENOM CEPH CEPH (92) 92 0.04 0.04 0 92 1 106 by freq Borderline 1.074 59 Tolerant 1 2.85 67 moderately conservative 138359 6p12.1 glutathione S-transferase A1 1716 rs1051612 POU1F1 5449 3 87408292 NM_000306 NP_000297 C/T Q4R plus 1527313 1303 SEQUENOM CEPH CEPH (92) 92 0.12 0.12 0 92 1 106 by freq Possibly damaging 1.696 22 conservative 173110 3p11 "POU domain, class 1, transcription factor 1 (Pit1, growth hormone factor 1)" 1717 rs1051623 CDH17 1015 8 95212362 NM_004063 NP_004054 C/G E734D minus 3523876 1303 SEQUENOM CEPH CEPH (92) 92 0.44 0.35 0.18 140 2 0.22 0.02 94 2 123 "by submitter,freq,cluster" Tolerant 0.23 3.03 13 conservative 603017 8q22.1 "cadherin 17, LI cadherin (liver-intestine)" 1718 rs1051623 CDH17 1015 8 95212362 NM_004063 NP_004054 C/G E734D minus 24044309 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.17 0.35 0.18 140 2 0.22 0.02 94 2 123 "by submitter,freq,cluster" Tolerant 0.23 3.03 13 conservative 603017 8q22.1 "cadherin 17, LI cadherin (liver-intestine)" 1719 rs1051624 CDH17 1015 8 95212348 NM_004063 NP_004054 A/C E739A minus 3525064 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.44 0.41 0.04 260 3 0.33 0.13 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 0.3 2.79 21 moderately radical 603017 8q22.1 "cadherin 17, LI cadherin (liver-intestine)" 1720 rs1051624 CDH17 1015 8 95212348 NM_004063 NP_004054 A/C E739A minus 3525064 1303 SEQUENOM CEPH CEPH (92) 92 0.37 0.41 0.04 260 3 0.33 0.13 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 0.3 2.79 21 moderately radical 603017 8q22.1 "cadherin 17, LI cadherin (liver-intestine)" 1721 rs1051624 CDH17 1015 8 95212348 NM_004063 NP_004054 A/C E739A minus 24497817 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.42 0.41 0.04 260 3 0.33 0.13 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 0.3 2.79 21 moderately radical 603017 8q22.1 "cadherin 17, LI cadherin (liver-intestine)" 1722 rs1051738 PDE4A 5141 19 10438843 NM_006202 NP_006193 A/C A497E plus 1527521 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.17 0.22 0.07 254 3 0.28 0.18 82 2 123 "HapMap,submitter,freq,cluster" Borderline 1.06 40 moderately radical 600126 19p13.2 "phosphodiesterase 4A, cAMP-specific (phosphodiesterase E2 dunce homolog, Drosophila)" 1723 rs1051738 PDE4A 5141 19 10438843 NM_006202 NP_006193 A/C A497E plus 14728683 1303 SEQUENOM CEPH CEPH (92) 92 0.29 0.22 0.07 254 3 0.28 0.18 82 2 123 "HapMap,submitter,freq,cluster" Borderline 1.06 40 moderately radical 600126 19p13.2 "phosphodiesterase 4A, cAMP-specific (phosphodiesterase E2 dunce homolog, Drosophila)" 1724 rs1051738 PDE4A 5141 19 10438843 NM_006202 NP_006193 A/C A497E plus 23646751 1371 PERLEGEN AFD_EUR_PANEL European American (24) 42 0.19 0.22 0.07 254 3 0.28 0.18 82 2 123 "HapMap,submitter,freq,cluster" Borderline 1.06 40 moderately radical 600126 19p13.2 "phosphodiesterase 4A, cAMP-specific (phosphodiesterase E2 dunce homolog, Drosophila)" 1725 rs1051740 EPHX1 2052 1 222326368 NM_000120 NP_000111 C/T Y113H plus 1527524 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 84 0.29 0.33 0.04 314 4 0.34 0.1 604 8 123 "HapMap,submitter,freq,cluster" Possibly damaging 1.928 14 Intolerant 0 2.81 24 moderately conservative 132810 1q42.1 "epoxide hydrolase 1, microsomal (xenobiotic)" 1726 rs1051740 EPHX1 2052 1 222326368 NM_000120 NP_000111 C/T Y113H plus 4041372 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.33 0.33 0.04 314 4 0.34 0.1 604 8 123 "HapMap,submitter,freq,cluster" Possibly damaging 1.928 14 Intolerant 0 2.81 24 moderately conservative 132810 1q42.1 "epoxide hydrolase 1, microsomal (xenobiotic)" 1727 rs1051740 EPHX1 2052 1 222326368 NM_000120 NP_000111 C/T Y113H plus 5586496 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.39 0.33 0.04 314 4 0.34 0.1 604 8 123 "HapMap,submitter,freq,cluster" Possibly damaging 1.928 14 Intolerant 0 2.81 24 moderately conservative 132810 1q42.1 "epoxide hydrolase 1, microsomal (xenobiotic)" 1728 rs1051740 EPHX1 2052 1 222326368 NM_000120 NP_000111 C/T Y113H plus 23857114 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.35 0.33 0.04 314 4 0.34 0.1 604 8 123 "HapMap,submitter,freq,cluster" Possibly damaging 1.928 14 Intolerant 0 2.81 24 moderately conservative 132810 1q42.1 "epoxide hydrolase 1, microsomal (xenobiotic)" 1729 rs1051881 EXOSC9 5393 4 123095570 NM_005033 NP_005024 C/G S341T plus 4478804 693 EGP_SNPS PDR90 NIHPDR 174 0.07 0.05 0.03 342 3 0.26 0.31 94 2 123 "HapMap,freq,cluster" moderately conservative 606180 4q27 "polymyositis/scleroderma autoantigen 1, 75kDa" 1730 rs1051881 EXOSC9 5393 4 123095570 NM_005033 NP_005024 C/G S341T plus 4478804 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.02 0.05 0.03 342 3 0.26 0.31 94 2 123 "HapMap,freq,cluster" moderately conservative 606180 4q27 "polymyositis/scleroderma autoantigen 1, 75kDa" 1731 rs1051881 EXOSC9 5393 4 123095570 NM_005033 NP_005024 C/G S341T plus 23305762 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.05 0.03 342 3 0.26 0.31 94 2 123 "HapMap,freq,cluster" moderately conservative 606180 4q27 "polymyositis/scleroderma autoantigen 1, 75kDa" 1732 rs1051931 PLA2G7 7941 6 46780902 NM_005084 NP_005075 A/G V379A plus 2226119 1303 SEQUENOM CEPH CEPH (92) 92 0.24 0.23 0.02 140 2 0.1 0.03 1390 3 123 "by doubleHit,freq,cluster" Possibly damaging 1.51 7 moderately conservative 601690 6p21.2-p12 "phospholipase A2, group VII (platelet-activating factor acetylhydrolase, plasma)" 1733 rs1051931 PLA2G7 7941 6 46780902 NM_005084 NP_005075 A/G V379A plus 23675802 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.23 0.02 140 2 0.1 0.03 1390 3 123 "by doubleHit,freq,cluster" Possibly damaging 1.51 7 moderately conservative 601690 6p21.2-p12 "phospholipase A2, group VII (platelet-activating factor acetylhydrolase, plasma)" 1734 rs1051992 PRKCDBP 112464 11 6297282 NM_145040 NP_659477 C/T L158P minus 16104065 1303 SEQUENOM CEPH CEPH (92) 92 0.4 0.41 0.01 140 2 0.37 0.02 94 2 123 "by doubleHit,freq,cluster" moderately conservative 11p15.4 "protein kinase C, delta binding protein" 1735 rs1051992 PRKCDBP 112464 11 6297282 NM_145040 NP_659477 C/T L158P minus 24514153 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.42 0.41 0.01 140 2 0.37 0.02 94 2 123 "by doubleHit,freq,cluster" moderately conservative 11p15.4 "protein kinase C, delta binding protein" 1736 rs1052576 CASP9 842 1 15577849 NM_001229 NP_001220 A/G Q221R minus 2924012 506 NCBI NIHPDR NIHPDR 826 0.45 0.45 0.02 1054 3 0.44 0.09 342 4 121 "by doubleHit,freq,cluster" Borderline 1.1 10 Tolerant 0.88 2.83 20 conservative 602234 1p36.3-p36.1 "caspase 9, apoptosis-related cysteine protease" 1737 rs1052576 CASP9 842 1 15577849 NM_001229 NP_001220 A/G Q221R minus 6310866 693 EGP_SNPS PDR90 NIHPDR 170 0.48 0.45 0.02 1054 3 0.44 0.09 342 4 121 "by doubleHit,freq,cluster" Borderline 1.1 10 Tolerant 0.88 2.83 20 conservative 602234 1p36.3-p36.1 "caspase 9, apoptosis-related cysteine protease" 1738 rs1052576 CASP9 842 1 15577849 NM_001229 NP_001220 A/G Q221R minus 6903699 775 SNP500CANCER CAUC1 Caucasian (31) 58 0.43 0.45 0.02 1054 3 0.44 0.09 342 4 121 "by doubleHit,freq,cluster" Borderline 1.1 10 Tolerant 0.88 2.83 20 conservative 602234 1p36.3-p36