PMID: 18485661

Genome-wide SNP typing reveals signatures of population history.

Genomics
AL Hughes, R Welch, V Puri, C Matthews, K Haque, SJ Chanock, M Yeager
2008-07

197 variants were identified in this publication


Variant ID Gene cDNA Protein Consequence Exon Intron
3-59887788-A-C FHIT c.348+20284T>G - IntronicSNV - 8/9
1-41978825-C-G HIVEP3 c.6067G>C p.Ala2023Pro Missense 8/9 -
5-26961133-C-T CDH9 c.228+27080G>A - IntronicSNV - 2/11
20-30109829-G-A HM13 c.184-5458G>A - IntronicSNV - 1/12
4-151888609-A-T LRBA c.217-38392T>A - IntronicSNV - 2/56
20-30109829-G-C HM13 c.184-5458G>C - IntronicSNV - 1/12
20-58582657-C-G CDH26 c.2295+815C>G - IntronicSNV - 17/17
4-151888609-A-G LRBA c.217-38392T>C - IntronicSNV - 2/56
3-41841716-A-C ULK4 c.1918T>G p.Ser640Ala Missense 20/37 -
20-30156378-T-G HM13 c.*347T>G - IntronicSNV - 12/12
7-8269678-T-C ICA1 c.184-1375A>G - IntronicSNV - 3/13
1-54060248-T-G GLIS1 c.328A>C p.Thr110Pro Missense 3/10 -
1-235976651-T-C LYST c.193-290A>G - IntronicSNV - 3/52
3-41288469-C-T ULK4 c.3779G>A p.Ser1260Asn Missense 37/37 -
1-235933535-C-G LYST c.5847G>C p.Gln1949His Missense 20/53 -
4-148810260-A-G ARHGAP10 c.1034+7177A>G - IntronicSNV - 10/22
14-67533273-G-C GPHN c.1144+7770G>C - IntronicSNV - 11/22
4-151850524-T-G LRBA c.217-307A>C - IntronicSNV - 2/56
4-42050768-A-G SLC30A9 c.738-626A>G - IntronicSNV - 8/17
4-42050768-A-T SLC30A9 c.738-626A>T - IntronicSNV - 8/17
15-29295870-T-C APBA2 c.-41+7861T>C - intron_variant - 2/13
9-95001109-C-T IARS c.3283+2029G>A - IntronicSNV - 30/33
1-235894473-C-T LYST c.8806G>A p.Val2936Ile Missense 35/53 -
8-42285336-G-C SLC20A2 c.1794+940C>G - IntronicSNV - 10/10
3-41860955-A-G ULK4 c.1808T>C p.Leu603Ser Missense 19/37 -
2-121696149-G-A GLI2 c.254+11107G>A - IntronicSNV - 3/13
11-88436209-A-T GRM5 c.912-49638T>A - IntronicSNV - 3/8
1-42180082-T-A HIVEP3 c.-800-13416A>T - intron_variant - 1/8
3-42569108-T-C VIPR1 c.503+120T>C - IntronicSNV - 5/12
4-42134066-C-T BEND4 c.1055-6375G>A - IntronicSNV - 3/5
4-169433326-T-A PALLD c.671T>A p.Met224Lys Missense 2/21 -
2-39664126-C-A MAP4K3 c.3G>T p.Met1Ile Missense 1/34 -
9-94988945-T-C IARS c.3409+2338A>G - IntronicSNV - 31/33
21-42583738-G-A BACE2 c.313-14455G>A - IntronicSNV - 1/8
16-24964518-T-C ARHGAP17 c.853-155A>G - IntronicSNV - 10/18
8-10935082-T-C XKR6 c.764+123003A>G - IntronicSNV - 1/2
4-151771968-A-C LRBA c.3912T>G p.Phe1304Leu Missense 24/57 -
5-26961885-G-A CDH9 c.228+26328C>T - IntronicSNV - 2/11
5-26961885-G-T CDH9 c.228+26328C>A - IntronicSNV - 2/11
2-121703133-G-C GLI2 c.255-5686G>C - IntronicSNV - 3/13
2-121732662-G-A GLI2 c.1345G>A p.Asp449Asn Missense 9/14 -
9-99614104-G-A ZNF782 c.15+125C>T - IntronicSNV - 3/5
21-42546817-C-T BACE2 c.312+6315C>T - IntronicSNV - 1/8
12-106763728-G-A POLR3B c.404+267G>A - IntronicSNV - 6/27
4-42011970-A-G SLC30A9 c.275-8158A>G - IntronicSNV - 2/17
21-42596837-G-A BACE2 c.313-1356G>A - IntronicSNV - 1/8
21-42596837-G-C BACE2 c.313-1356G>C - IntronicSNV - 1/8
14-66986613-A-T GPHN c.64+11304A>T - IntronicSNV - 1/22
14-66986613-A-G GPHN c.64+11304A>G - IntronicSNV - 1/22
14-66986613-A-C GPHN c.64+11304A>C - IntronicSNV - 1/22
4-42011970-A-T SLC30A9 c.275-8158A>T - IntronicSNV - 2/17
15-29261716-C-T APBA2 c.-94-26240C>T - intron_variant - 1/13
8-11058427-C-T XKR6 c.422G>A p.Gly141Glu Missense 1/3 -
15-72612212-C-T CELF6 c.4G>A p.Ala2Thr Missense 1/13 -
14-67253035-G-A GPHN c.201+9796G>A - IntronicSNV - 3/22
3-59880384-T-C FHIT c.348+27688A>G - IntronicSNV - 8/9
5-26988328-G-T CDH9 c.113C>A p.Ala38Glu Missense 2/12 -
5-26988328-G-A CDH9 c.113C>T p.Ala38Val Missense 2/12 -
4-151199080-G-A LRBA c.8390C>T p.Ser2797Leu Missense 56/57 -
1-42050366-C-T HIVEP3 c.103G>A p.Val35Ile Missense 4/9 -
14-67443159-T-A GPHN c.963+11117T>A - IntronicSNV - 9/22
9-99581916-C-G ZNF782 c.389G>C p.Arg130Pro Missense 6/6 -
1-235887276-G-C LYST c.9315+52C>G - IntronicSNV - 39/52
4-151773593-G-C LRBA c.3269C>G p.Ala1090Gly Missense 23/57 -
9-95007341-A-G IARS c.2804T>C p.Val935Ala Missense 27/34 -
4-148687639-T-C ARHGAP10 c.154+34033T>C - IntronicSNV - 1/22
4-148687639-T-G ARHGAP10 c.154+34033T>G - IntronicSNV - 1/22
12-106848414-A-G POLR3B c.2218A>G p.Thr740Ala Missense 20/28 -
11-88378005-A-G GRM5 c.1147+8331T>C - IntronicSNV - 4/8
9-99581916-C-T ZNF782 c.389G>A p.Arg130His Missense 6/6 -
1-235887276-G-T LYST c.9315+52C>A - IntronicSNV - 39/52
2-121703623-A-C GLI2 c.255-5196A>C - IntronicSNV - 3/13
4-42134066-C-A BEND4 c.1055-6375G>T - IntronicSNV - 3/5
4-148696917-T-C ARHGAP10 c.154+43311T>C - IntronicSNV - 1/22
1-41976529-C-G HIVEP3 c.6814G>C p.Gly2272Arg Missense 9/9 -
6-69801042-C-G ADGRB3 c.2480+15112C>G - IntronicSNV - 17/31
1-42202714-T-C HIVEP3 c.-800-36048A>G - intron_variant - 1/8
4-148665206-A-G ARHGAP10 c.154+11600A>G - IntronicSNV - 1/22
1-42047208-C-G HIVEP3 c.3261G>C p.Gln1087His Missense 4/9 -
12-123651966-G-C MPHOSPH9 c.2457-630C>G - IntronicSNV - 16/23
9-99581811-C-A ZNF782 c.494G>T p.Arg165Leu Missense 6/6 -
6-69801042-C-T ADGRB3 c.2480+15112C>T - IntronicSNV - 17/31
6-69801042-C-A ADGRB3 c.2480+15112C>A - IntronicSNV - 17/31
20-58587709-C-T CDH26 c.2423C>T p.Pro808Leu Missense 18/18 -
12-123651162-A-G MPHOSPH9 c.2591+40T>C - IntronicSNV - 17/23
1-42048745-T-C HIVEP3 c.1724A>G p.His575Arg Missense 4/9 -
9-117691558-C-A TNFSF8 c.195+831G>T - IntronicSNV - 1/3
9-99583468-C-A ZNF782 c.245-1408G>T - IntronicSNV - 5/5
9-99583468-C-G ZNF782 c.245-1408G>C - IntronicSNV - 5/5
14-67482629-A-G GPHN c.964-7721A>G - IntronicSNV - 9/22
8-56207821-A-G XKR4 c.807-62417A>G - IntronicSNV - 1/2
9-99581811-C-T ZNF782 c.494G>A p.Arg165His Missense 6/6 -
15-29399005-T-G APBA2 c.1900T>G p.Cys634Gly Missense 11/14 -
9-99584880-G-A ZNF782 c.245-2820C>T - IntronicSNV - 5/5
1-42097678-G-T HIVEP3 c.1-47210C>A - IntronicSNV - 1/8
1-42097678-G-A HIVEP3 c.1-47210C>T - IntronicSNV - 1/8
20-58583207-A-G CDH26 c.2295+1365A>G - IntronicSNV - 17/17
8-56344186-C-T XKR4 c.1006+73749C>T - IntronicSNV - 2/2
17-53828493-A-C PCTP c.29A>C p.Glu10Ala Missense 1/6 -
15-29347019-T-C APBA2 c.932T>C p.Leu311Pro Missense 3/14 -
1-235976594-C-T LYST c.193-233G>A - IntronicSNV - 3/52
1-42048745-T-A HIVEP3 c.1724A>T p.His575Leu Missense 4/9 -
2-121742236-C-T GLI2 c.1873C>T p.Pro625Ser Missense 12/14 -
1-41976328-T-C HIVEP3 c.7015A>G p.Thr2339Ala Missense 9/9 -
1-41976328-T-A HIVEP3 c.7015A>T p.Thr2339Ser Missense 9/9 -
2-121742099-G-T GLI2 c.1736G>T p.Ser579Ile Missense 12/14 -
15-72579646-A-G CELF6 c.1406T>C p.Val469Ala Missense 12/13 -
4-151207127-C-T LRBA c.8074G>A p.Ala2692Thr Missense 54/57 -
3-41877414-T-C ULK4 c.1706A>G p.Lys569Arg Missense 18/37 -
4-124021417-C-T SPATA5 c.2340+9557C>T - IntronicSNV - 14/15
1-54065523-T-C GLIS1 c.-89+251A>G - intron_variant - 2/9
8-10953092-T-C XKR6 c.764+104993A>G - IntronicSNV - 1/2
1-235947510-A-T LYST c.4863-2123T>A - IntronicSNV - 14/52
1-235947510-A-G LYST c.4863-2123T>C - IntronicSNV - 14/52
8-10953092-T-A XKR6 c.764+104993A>T - IntronicSNV - 1/2
1-42182144-T-C HIVEP3 c.-800-15478A>G - intron_variant - 1/8
4-42067352-T-C SLC30A9 c.1058T>C p.Leu353Ser Missense 12/18 -
14-67638455-C-T GPHN c.2079+2702C>T - IntronicSNV - 21/22
14-67638455-C-A GPHN c.2079+2702C>A - IntronicSNV - 21/22
14-67638455-C-G GPHN c.2079+2702C>G - IntronicSNV - 21/22
15-72578072-C-A CELF6 c.*640G>T - 3_prime_UTR_variant 13/13 -
16-24964716-G-T ARHGAP17 c.853-353C>A - IntronicSNV - 10/18
7-8198186-G-T ICA1 c.676C>A p.Leu226Ile Missense 7/14 -
17-53842322-C-T PCTP c.142-2374C>T - IntronicSNV - 1/5
4-169784731-T-C PALLD c.1965-27342T>C - IntronicSNV - 10/20
4-169433327-G-A PALLD c.672G>A p.Met224Ile Missense 2/21 -
6-112010425-G-A FYN c.1273+5153C>T - IntronicSNV - 12/13
8-42306813-T-C SLC20A2 c.614-4533A>G - IntronicSNV - 5/10
3-41725005-A-G ULK4 c.2782-1710T>C - IntronicSNV - 27/36
8-56260400-G-A XKR4 c.807-9838G>A - IntronicSNV - 1/2
2-121702776-G-A GLI2 c.255-6043G>A - IntronicSNV - 3/13
1-41976529-C-T HIVEP3 c.6814G>A p.Gly2272Arg Missense 9/9 -
9-94985637-T-C IARS c.3544A>G p.Lys1182Glu Missense 32/34 -
4-148687639-T-A ARHGAP10 c.154+34033T>A - IntronicSNV - 1/22
4-148821136-A-T ARHGAP10 c.1035-6653A>T - IntronicSNV - 10/22
3-54912359-G-A CACNA2D3 c.1711-686G>A - IntronicSNV - 18/37
2-39608782-G-C MAP4K3 c.97-3518C>G - IntronicSNV - 1/33
4-42003671-A-G SLC30A9 c.148A>G p.Met50Val Missense 2/18 -
2-121703623-A-G GLI2 c.255-5196A>G - IntronicSNV - 3/13
2-121696011-T-G GLI2 c.254+10969T>G - IntronicSNV - 3/13
16-24942275-C-T ARHGAP17 c.2111G>A p.Gly704Asp Missense 18/19 -
2-121696023-C-T GLI2 c.254+10981C>T - IntronicSNV - 3/13
2-39611382-T-C MAP4K3 c.97-6118A>G - IntronicSNV - 1/33
4-151840752-A-G LRBA c.645+1598T>C - IntronicSNV - 5/56
3-59887788-A-G FHIT c.348+20284T>C - IntronicSNV - 8/9
1-54070831-T-C GLIS1 c.-266-4880A>G - intron_variant - 1/9
5-132109742-G-A SEPT8 c.30+3058C>T - IntronicSNV - 1/9
14-67197950-T-A GPHN c.144-45232T>A - IntronicSNV - 2/22
5-26988424-T-C CDH9 c.17A>G p.Tyr6Cys Missense 2/12 -
4-42089177-G-A SLC30A9 c.*1034G>A - 3-UTRSNV 18/18 -
4-42003671-A-C SLC30A9 c.148A>C p.Met50Leu Missense 2/18 -
2-121732662-G-C GLI2 c.1345G>C p.Asp449His Missense 9/14 -
2-121732662-G-T GLI2 c.1345G>T p.Asp449Tyr Missense 9/14 -
14-67379015-A-C GPHN c.390-3705A>C - IntronicSNV - 5/22
15-72600493-A-C CELF6 c.346-3358T>G - IntronicSNV - 2/12
3-41925398-C-T ULK4 c.1624G>A p.Ala542Thr Missense 17/37 -
12-123645831-G-T MPHOSPH9 c.3233C>A p.Ala1078Asp Missense 22/24 -
9-117667443-T-C TNFSF8 c.310+665A>G - IntronicSNV - 3/3
7-8268155-T-C ICA1 c.256+76A>G - IntronicSNV - 4/13
6-69817329-G-A ADGRB3 c.2480+31399G>A - IntronicSNV - 17/31
3-41288466-G-A ULK4 c.3782C>T p.Ala1261Val Missense 37/37 -
6-70071402-G-C ADGRB3 c.4237G>C p.Glu1413Gln Missense 29/32 -
1-42050035-A-T HIVEP3 c.434T>A p.Leu145His Missense 4/9 -
3-41925398-C-G ULK4 c.1624G>C p.Ala542Pro Missense 17/37 -
2-121702919-A-G GLI2 c.255-5900A>G - IntronicSNV - 3/13
8-10953092-T-G XKR6 c.764+104993A>C - IntronicSNV - 1/2
2-121702776-G-C GLI2 c.255-6043G>C - IntronicSNV - 3/13
9-94988945-T-A IARS c.3409+2338A>T - IntronicSNV - 31/33
4-151749473-T-C LRBA c.5030A>G p.Asn1677Ser Missense 30/57 -
1-54060248-T-C GLIS1 c.328A>G p.Thr110Ala Missense 3/10 -
15-29398915-G-T APBA2 c.1810G>T p.Gly604Cys Missense 11/14 -
15-29398915-G-A APBA2 c.1810G>A p.Gly604Ser Missense 11/14 -
11-130278924-T-A ADAMTS8 c.1751-89A>T - IntronicSNV - 6/8
3-41831203-C-T ULK4 c.2143G>A p.Ala715Thr Missense 21/37 -
9-117691558-C-T TNFSF8 c.195+831G>A - IntronicSNV - 1/3
17-53828493-A-G PCTP c.29A>G p.Glu10Gly Missense 1/6 -
17-53828493-A-T PCTP c.29A>T p.Glu10Val Missense 1/6 -
4-151771970-A-C LRBA c.3910T>G p.Phe1304Val Missense 24/57 -
11-130278924-T-G ADAMTS8 c.1751-89A>C - IntronicSNV - 6/8
20-30137904-C-T HM13 c.704C>T p.Ser235Phe Missense 7/13 -
17-53846348-T-C PCTP c.259+1535T>C - IntronicSNV - 2/5
14-67606768-C-T GPHN c.1749-3311C>T - IntronicSNV - 17/22
4-151656589-C-T LRBA c.5646-71G>A - IntronicSNV - 35/56
4-151781297-T-C LRBA c.2767-7202A>G - IntronicSNV - 22/56
3-41831203-C-A ULK4 c.2143G>T p.Ala715Ser Missense 21/37 -
16-24942275-C-G ARHGAP17 c.2111G>C p.Gly704Ala Missense 18/19 -
4-124235172-C-T SPATA5 c.2635C>T p.Arg879Cys Missense 16/16 -
20-58587672-C-T CDH26 c.2386C>T p.Leu796Phe Missense 18/18 -
12-106809177-T-G POLR3B c.1101+4439T>G - IntronicSNV - 12/27
4-169433326-T-C PALLD c.671T>C p.Met224Thr Missense 2/21 -
5-31428028-C-T DROSHA c.3216+1554G>A - IntronicSNV - 26/34
1-42180082-T-C HIVEP3 c.-800-13416A>G - intron_variant - 1/8
5-132107051-G-T SEPT8 c.30+5749C>A - IntronicSNV - 1/9
11-88380387-C-T GRM5 c.1147+5949G>A - IntronicSNV - 4/8
4-124021864-A-G SPATA5 c.2340+10004A>G - IntronicSNV - 14/15
20-30154237-G-C HM13 c.1034+139G>C - IntronicSNV - 11/12
2-121701289-T-C GLI2 c.255-7530T>C - IntronicSNV - 3/13