PMID: 17999355

A genomewide association study of skin pigmentation in a South Asian population.

American journal of human genetics
RP Stokowski, PV Pant, T Dadd, A Fereday, DA Hinds, C Jarman, W Filsell, RS Ginger, MR Green, FJ van der Ouderaa, DR Cox
2007-12

194 variants were identified in this publication


Variant ID Gene cDNA Protein Consequence Exon Intron
15-49221881-G-A SHC4 c.586-4735C>T - IntronicSNV - 1/11
15-50400050-G-C ATP8B4 c.1-887C>G - IntronicSNV - 1/27
15-50392995-C-G ATP8B4 c.28+6141G>C - IntronicSNV - 2/27
15-50399242-A-T ATP8B4 c.1-79T>A - IntronicSNV 1/28 -
15-28200408-T-C OCA2 c.1785-47A>G - IntronicSNV - 16/23
15-49039797-T-C CEP152 c.3467-2608A>G - IntronicSNV - 21/25
15-49039797-T-A CEP152 c.3467-2608A>T - IntronicSNV - 21/25
15-50269673-G-A ATP8B4 c.1034+2141C>T - IntronicSNV - 12/27
9-12699776-T-C TYRP1 c.913+1121T>C - IntronicSNV - 4/7
15-50197870-A-C ATP8B4 c.2142-4434T>G - IntronicSNV - 20/27
9-12709586-A-T TYRP1 c.*404A>T - 3-UTRSNV 8/8 -
15-50497848-G-T SLC27A2 c.972+288G>T - IntronicSNV - 4/9
5-33951551-A-G SLC45A2 c.1156+108T>C - IntronicSNV - 5/6
11-88961188-G-A TYR c.1184+50G>A - IntronicSNV - 3/4
15-49582589-C-G GALK2 c.724-1935C>G - IntronicSNV - 7/9
15-50221945-A-G ATP8B4 c.1642+1371T>C - IntronicSNV - 16/27
15-28273350-T-C OCA2 c.327-145A>G - IntronicSNV - 3/23
11-88911696-C-A TYR c.575C>A p.Ser192Tyr Missense 1/5 -
15-49916655-T-G DTWD1 c.1-710T>G - IntronicSNV - 2/5
15-49049823-C-T CEP152 c.2695-1073G>A - IntronicSNV - 19/25
15-50500984-G-A SLC27A2 c.972+3424G>A - IntronicSNV - 4/9
15-49676102-T-A FAM227B c.1013-12506A>T - IntronicSNV - 11/15
15-49676102-T-C FAM227B c.1013-12506A>G - IntronicSNV - 11/15
15-49704741-G-A FAM227B c.1013-41145C>T - IntronicSNV - 11/15
15-28202573-G-A OCA2 c.1784+161C>T - IntronicSNV - 16/23
15-48034025-C-T SEMA6D c.1-17971C>T - IntronicSNV - 1/12
15-50283661-T-C ATP8B4 c.590-3915A>G - IntronicSNV - 9/27
20-32856998-A-G ASIP c.*25A>G - 3-UTRSNV 3/3 -
15-49075229-T-G CEP152 c.1322-802A>C - IntronicSNV - 10/25
15-49199392-G-A SHC4 c.657-16384C>T - IntronicSNV - 2/11
15-48798910-A-G FBN1 c.1838-1566T>C - IntronicSNV - 15/65
15-48526362-G-T SLC12A1 c.1088-712G>T - IntronicSNV - 8/26
15-49206797-A-G SHC4 c.656+10279T>C - IntronicSNV - 2/11
15-49032699-C-T CEP152 c.3925+1099G>A - IntronicSNV - 25/25
15-50212281-A-G ATP8B4 c.1923+162T>C - IntronicSNV - 18/27
15-50212281-A-C ATP8B4 c.1923+162T>G - IntronicSNV - 18/27
15-49056670-T-G CEP152 c.2281-1801A>C - IntronicSNV - 17/25
15-50163808-G-A ATP8B4 c.3027+4667C>T - IntronicSNV - 25/27
16-89986546-G-A MC1R c.880G>A p.Asp294Asn Missense 1/1 -
15-48574956-C-T SLC12A1 c.2486-2347C>T - IntronicSNV - 20/26
9-12704725-C-T TYRP1 c.1261+20C>T - IntronicSNV - 6/7
15-48724696-T-C FBN1 c.6739+367A>G - IntronicSNV - 55/65
15-50275011-C-T ATP8B4 c.749-1520G>A - IntronicSNV - 10/27
15-49047492-A-G CEP152 c.3345+608T>C - IntronicSNV - 20/25
15-48052595-A-C SEMA6D c.204A>C p.Thr68Thr Synonymous 3/13 -
15-48033368-G-A SEMA6D c.1-18628G>A - IntronicSNV - 1/12
15-48524522-G-C SLC12A1 c.976-402G>C - IntronicSNV - 7/26
15-49136026-G-A SHC4 c.1304-241C>T - IntronicSNV - 9/11
15-50171847-C-T ATP8B4 c.2698-191G>A - IntronicSNV - 23/27
15-48057619-C-T SEMA6D c.*362C>T - 3-UTRSNV 13/13 -
15-48524522-G-A SLC12A1 c.976-402G>A - IntronicSNV - 7/26
15-50315253-G-A ATP8B4 c.363-12139C>T - IntronicSNV - 6/27
15-50151263-G-T ATP8B4 c.*1128C>A - 3-UTRSNV 28/28 -
15-50151263-G-A ATP8B4 c.*1128C>T - 3-UTRSNV 28/28 -
13-95095529-A-G DCT c.1480+161T>C - IntronicSNV - 9/9
15-49813343-T-C FAM227B c.875-12798A>G - IntronicSNV - 10/15
15-50297709-A-G ATP8B4 c.436-3289T>C - IntronicSNV - 7/27
15-50297709-A-T ATP8B4 c.436-3289T>A - IntronicSNV - 7/27
15-49162953-T-C SHC4 c.894+1333A>G - IntronicSNV - 5/11
15-48029014-T-C SEMA6D c.-55+17944T>C - intron_variant - 1/12
13-95095529-A-T DCT c.1480+161T>A - IntronicSNV - 9/9
15-48042146-A-G SEMA6D c.1-9850A>G - IntronicSNV - 1/12
15-49060083-G-A CEP152 c.2018+333C>T - IntronicSNV - 15/25
15-48720652-C-T FBN1 c.6888G>A p.Gln2296Gln Synonymous 57/66 -
11-89018440-A-G TYR c.1366+318A>G - IntronicSNV - 4/4
15-49224372-G-A SHC4 c.586-7226C>T - IntronicSNV - 1/11
15-49098016-C-A CEP152 c.1-170G>T - IntronicSNV - 1/25
15-50197656-A-G ATP8B4 c.2142-4220T>C - IntronicSNV - 20/27
15-49184681-G-A SHC4 c.657-1673C>T - IntronicSNV - 2/11
15-49187674-G-A SHC4 c.657-4666C>T - IntronicSNV - 2/11
15-48722884-A-G FBN1 c.6855T>C p.Asp2285Asp Synonymous 56/66 -
15-50256379-G-C ATP8B4 c.1244-2162C>G - IntronicSNV - 13/27
16-89985918-C-G MC1R c.252C>G p.Asp84Glu Missense 1/1 -
15-48757460-T-C FBN1 c.4942+305A>G - IntronicSNV - 40/65
15-48633153-C-T DUT c.557-333C>T - IntronicSNV - 4/6
15-28202625-C-T OCA2 c.1784+109G>A - IntronicSNV - 16/23
15-28202625-C-A OCA2 c.1784+109G>T - IntronicSNV - 16/23
15-48053229-C-A SEMA6D c.276C>A p.Pro92Pro Synonymous 4/13 -
15-49103244-T-C CEP152 c.-94A>G - 5_prime_UTR_variant 1/26 -
15-50311148-A-T ATP8B4 c.363-8034T>A - IntronicSNV - 6/27
15-48873615-G-C FBN1 c.538+14865C>G - IntronicSNV - 6/65
15-50311148-A-G ATP8B4 c.363-8034T>C - IntronicSNV - 6/27
15-48873615-G-A FBN1 c.538+14865C>T - IntronicSNV - 6/65
15-49438326-T-G COPS2 c.55-1051A>C - IntronicSNV - 1/12
15-49438326-T-C COPS2 c.55-1051A>G - IntronicSNV - 1/12
15-50197870-A-G ATP8B4 c.2142-4434T>C - IntronicSNV - 20/27
15-28196885-C-G OCA2 c.1951+45G>C - IntronicSNV - 18/23
15-28196885-C-T OCA2 c.1951+45G>A - IntronicSNV - 18/23
15-49424366-A-G COPS2 c.948-1353T>C - IntronicSNV - 9/12
15-48864877-T-C FBN1 c.538+23603A>G - IntronicSNV - 6/65
5-33964210-T-G SLC45A2 c.563-89A>C - IntronicSNV - 2/6
15-28235773-C-T OCA2 c.1065G>A p.Ala355Ala Synonymous 10/24 -
15-50302864-T-C ATP8B4 c.435+178A>G - IntronicSNV - 7/27
11-89018440-A-T TYR c.1366+318A>T - IntronicSNV - 4/4
15-50486387-C-T SLC27A2 c.479-3310C>T - IntronicSNV - 1/9
15-48027204-A-C SEMA6D c.-55+16134A>C - intron_variant - 1/12
15-50486387-C-G SLC27A2 c.479-3310C>G - IntronicSNV - 1/9
15-48049776-C-A SEMA6D c.1-2220C>A - IntronicSNV - 1/12
15-48049776-C-T SEMA6D c.1-2220C>T - IntronicSNV - 1/12
15-50388921-A-G ATP8B4 c.28+10215T>C - IntronicSNV - 2/27
15-50353277-T-A ATP8B4 c.87+13047A>T - IntronicSNV - 3/27
15-48056219-A-G SEMA6D c.920A>G p.Asn307Ser Missense 10/13 -
15-50366910-G-A ATP8B4 c.29-528C>T - IntronicSNV - 2/27
15-49099915-C-T CEP152 c.1-2069G>A - IntronicSNV - 1/25
15-50193553-G-A ATP8B4 c.2142-117C>T - IntronicSNV - 20/27
15-49740304-A-C FGF7 c.286+23524A>C - IntronicSNV - 2/3
13-95095391-A-T DCT c.1480+299T>A - IntronicSNV - 9/9
15-49152007-C-G SHC4 c.947-1995G>C - IntronicSNV - 6/11
15-49101831-G-A CEP152 c.-8+1327C>T - intron_variant - 1/25
15-49206902-A-T SHC4 c.656+10174T>A - IntronicSNV - 2/11
15-49206902-A-G SHC4 c.656+10174T>C - IntronicSNV - 2/11
15-49760425-G-T FGF7 c.287-14923G>T - IntronicSNV - 2/3
15-50353277-T-G ATP8B4 c.87+13047A>C - IntronicSNV - 3/27
15-48720652-C-A FBN1 c.6888G>T p.Gln2296His Missense 57/66 -
15-49176203-A-T SHC4 c.840+242T>A - IntronicSNV - 4/11
15-49143232-G-T SHC4 c.1303+153C>A - IntronicSNV - 9/11
5-33947544-C-A SLC45A2 c.1157-65G>T - IntronicSNV - 5/6
15-49530321-T-A GALK2 c.325-1097T>A - IntronicSNV - 4/9
15-50267897-A-T ATP8B4 c.1035-2910T>A - IntronicSNV - 12/27
15-48487854-C-T CTXN2 c.-58+3804C>T - intron_variant - 1/1
15-49530321-T-G GALK2 c.325-1097T>G - IntronicSNV - 4/9
15-49737696-A-G FGF7 c.286+20916A>G - IntronicSNV - 2/3
15-48747440-C-T FBN1 c.5422+1394G>A - IntronicSNV - 44/65
15-50192977-G-T ATP8B4 c.2289+312C>A - IntronicSNV - 21/27
15-50192977-G-A ATP8B4 c.2289+312C>T - IntronicSNV - 21/27
15-49215309-C-T SHC4 c.656+1767G>A - IntronicSNV - 2/11
15-48043458-T-C SEMA6D c.1-8538T>C - IntronicSNV - 1/12
15-49095202-T-G CEP152 c.87+2558A>C - IntronicSNV - 2/25
15-49227821-C-G SHC4 c.586-10675G>C - IntronicSNV - 1/11
15-49253477-A-T SHC4 c.585+1151T>A - IntronicSNV - 1/11
15-49813115-T-C FAM227B c.875-12570A>G - IntronicSNV - 10/15
15-49253477-A-G SHC4 c.585+1151T>C - IntronicSNV - 1/11
15-49253477-A-C SHC4 c.585+1151T>G - IntronicSNV - 1/11
15-50193553-G-C ATP8B4 c.2142-117C>G - IntronicSNV - 20/27
15-50497294-A-G SLC27A2 c.848-142A>G - IntronicSNV - 3/9
9-12704725-C-A TYRP1 c.1261+20C>A - IntronicSNV - 6/7
5-33963870-C-T SLC45A2 c.814G>A p.Glu272Lys Missense 3/7 -
15-49075918-T-C CEP152 c.1321+252A>G - IntronicSNV - 10/25
15-49075918-T-A CEP152 c.1321+252A>T - IntronicSNV - 10/25
15-50151529-G-A ATP8B4 c.*862C>T - 3-UTRSNV 28/28 -
9-12704725-C-G TYRP1 c.1261+20C>G - IntronicSNV - 6/7
15-48864477-T-C FBN1 c.538+24003A>G - IntronicSNV - 6/65
13-95095331-T-C DCT c.1480+359A>G - IntronicSNV - 9/9
15-50268059-G-A ATP8B4 c.1035-3072C>T - IntronicSNV - 12/27
15-49624784-G-A FAM227B c.1350-738C>T - IntronicSNV - 14/15
13-95090692-T-A DCT c.*1460A>T - IntergenicSNV 10/10 -
13-95090692-T-G DCT c.*1460A>C - IntergenicSNV 10/10 -
15-48433353-A-C SLC24A5 c.1122A>C p.Leu374Phe Missense 8/9 -
15-49624784-G-C FAM227B c.1350-738C>G - IntronicSNV - 14/15
15-48035191-C-T SEMA6D c.1-16805C>T - IntronicSNV - 1/12
16-89985997-G-A MC1R c.331G>A p.Ala111Thr Missense 1/1 -
15-49713221-A-T FAM227B c.1013-49625T>A - IntronicSNV - 11/15
15-48027328-C-G SEMA6D c.-55+16258C>G - intron_variant - 1/12
15-48433353-A-T SLC24A5 c.1122A>T p.Leu374Phe Missense 8/9 -
15-49713221-A-G FAM227B c.1013-49625T>C - IntronicSNV - 11/15
15-49227821-C-T SHC4 c.586-10675G>A - IntronicSNV - 1/11
13-95089735-T-C DCT c.*2417A>G - IntergenicSNV 10/10 -
15-49562732-C-T GALK2 c.472-11452C>T - IntronicSNV - 5/9
15-49304325-G-C SECISBP2L c.1597-265C>G - IntronicSNV - 11/16
15-28089922-C-T OCA2 c.2432+183G>A - IntronicSNV - 23/23
16-89986777-C-A MC1R c.*157C>A - 3-UTRSNV 1/1 -
15-48797146-C-T FBN1 c.1960+76G>A - IntronicSNV - 16/65
15-49231514-G-C SHC4 c.586-14368C>G - IntronicSNV - 1/11
15-49231514-G-A SHC4 c.586-14368C>T - IntronicSNV - 1/11
15-48039088-A-T SEMA6D c.1-12908A>T - IntronicSNV - 1/12
9-12708910-C-G TYRP1 c.1409-67C>G - IntronicSNV - 7/7
15-49238430-C-T SHC4 c.585+16198G>A - IntronicSNV - 1/11
15-49090175-G-A CEP152 c.161C>T p.Ser54Leu Missense 3/26 -
15-49548851-A-G GALK2 c.471+17287A>G - IntronicSNV - 5/9
15-49420816-A-G COPS2 c.1187+83T>C - IntronicSNV - 12/12
15-48572635-A-G SLC12A1 c.2486-4668A>G - IntronicSNV - 20/26
16-89986608-A-G MC1R c.942A>G p.Thr314Thr Synonymous 1/1 -
15-49060083-G-T CEP152 c.2018+333C>A - IntronicSNV - 15/25
15-50350684-C-T ATP8B4 c.88-11023G>A - IntronicSNV - 3/27
16-89985131-C-T MC1R c.1-536C>T - 5-UTRSNV 1/1 -
15-28228644-G-A OCA2 c.1365-15C>T - IntronicSNV - 13/23
15-49192326-T-C SHC4 c.657-9318A>G - IntronicSNV - 2/11
15-48770961-A-C FBN1 c.3964+2891T>G - IntronicSNV - 32/65
15-49916720-T-C DTWD1 c.1-645T>C - IntronicSNV - 1/5
15-49151403-C-T SHC4 c.947-1391G>A - IntronicSNV - 6/11
12-56351346-G-A PMEL c.741C>T p.Pro247Pro Synonymous 7/12 -
15-48024922-A-G SEMA6D c.-55+13852A>G - intron_variant - 1/12
15-50297052-A-C ATP8B4 c.436-2632T>G - IntronicSNV - 7/27
15-48057619-C-G SEMA6D c.*362C>G - 3-UTRSNV 13/13 -
16-89986777-C-T MC1R c.*157C>T - 3-UTRSNV 1/1 -
5-33964210-T-A SLC45A2 c.563-89A>T - IntronicSNV - 2/6
15-50170441-C-T ATP8B4 c.2781+1132G>A - IntronicSNV - 24/27
15-49734843-A-G FGF7 c.286+18063A>G - IntronicSNV - 2/3
15-49641887-A-G FAM227B c.1272-14194T>C - IntronicSNV - 13/15
16-89987201-A-G MC1R c.*581A>G - 3-UTRSNV 1/1 -
9-12705095-T-G TYRP1 c.1261+390T>G - IntronicSNV - 6/7
16-89986117-C-A MC1R c.451C>A p.Arg151Ser Missense 1/1 -
16-89986117-C-G MC1R c.451C>G p.Arg151Gly Missense 1/1 -
15-49074539-C-T CEP152 c.1322-112G>A - IntronicSNV - 10/25