rs12638941

Homo sapiens
C>T
SLC6A6 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0487 (14578/29880,GnomAD)
T=0422 (12313/29118,TOPMED)
C==0453 (2269/5008,1000G)
C==0430 (1656/3854,ALSPAC)
C==0433 (1604/3708,TWINSUK)
chr3:14419407 (GRCh38.p7) (3p25.1)
ND
GWASdb2
1   publication(s)
See rs on genome
453 Enhancers around
9 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 3NC_000003.12:g.14419407C>T
GRCh37.p13 chr 3NC_000003.11:g.14460915C>T

Gene: SLC6A6, solute carrier family 6 member 6(plus strand)

Molecule type Change Amino acid[Codon] SO Term
SLC6A6 transcript variant 2NM_001134367.3:c.N/AIntron Variant
SLC6A6 transcript variant 3NM_001134368.3:c.N/AIntron Variant
SLC6A6 transcript variant 1NM_003043.5:c.N/AIntron Variant
SLC6A6 transcript variant 4NR_103507.2:n.N/AIntron Variant
SLC6A6 transcript variant X4XM_011534031.2:c.N/AIntron Variant
SLC6A6 transcript variant X1XM_006713307.2:c.N/AGenic Upstream Transcript Variant
SLC6A6 transcript variant X2XM_011534030.2:c.N/AGenic Upstream Transcript Variant
SLC6A6 transcript variant X5XR_427286.2:n.N/AGenic Upstream Transcript Variant
SLC6A6 transcript variant X3XR_940495.2:n.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.835T=0.165
1000GenomesAmericanSub694C=0.430T=0.570
1000GenomesEast AsianSub1008C=0.092T=0.908
1000GenomesEuropeSub1006C=0.447T=0.553
1000GenomesGlobalStudy-wide5008C=0.453T=0.547
1000GenomesSouth AsianSub978C=0.330T=0.670
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.430T=0.570
The Genome Aggregation DatabaseAfricanSub8702C=0.786T=0.214
The Genome Aggregation DatabaseAmericanSub836C=0.420T=0.580
The Genome Aggregation DatabaseEast AsianSub1614C=0.072T=0.928
The Genome Aggregation DatabaseEuropeSub18426C=0.428T=0.571
The Genome Aggregation DatabaseGlobalStudy-wide29880C=0.512T=0.487
The Genome Aggregation DatabaseOtherSub302C=0.360T=0.640
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.577T=0.422
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.433T=0.567
PMID Title Author Journal
19268276Genome-wide association study of smoking initiation and current smoking.Vink JMAm J Hum Genet

P-Value

SNP ID p-value Traits Study
rs126389410.000705nicotine smoking19268276

eQTL of rs12638941 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
There is no eQTL annotation for this SNP

meQTL of rs12638941 in Fetal Brain

Probe ID Position Gene beta p-value
There is no meQTL annotation for this SNP

Genomic View

Chromatin Interaction

There is no significant Hi-C chromatin interaction data for this SNP.

Enhancer Annotation (GRCh37.p13)

Chromosome Start End Region Distance ( -/+ : Up/Downstream )
chr31443259514433182E067-27733
chr31443319814433354E067-27561
chr31444680714446997E067-13918
chr31444705814447234E067-13681
chr31444739214447646E067-13269
chr31445434114455584E067-5331
chr31447263614475032E06711721
chr31447520014476695E06714285
chr31447695914477550E06716044
chr31447772214478031E06716807
chr31447814314478565E06717228
chr31448042014480478E06719505
chr31448061414480676E06719699
chr31448075714480851E06719842
chr31448088014481468E06719965
chr31448173814481949E06720823
chr31448204214482400E06721127
chr31448251914482866E06721604
chr31448305414483104E06722139
chr31448316414483347E06722249
chr31448335114483486E06722436
chr31448354714483698E06722632
chr31448379014483840E06722875
chr31448408814484138E06723173
chr31448435714484469E06723442
chr31449031814490456E06729403
chr31449066814490807E06729753
chr31449086914491069E06729954
chr31449318314493247E06732268
chr31449327614493453E06732361
chr31449346014495149E06732545
chr31449522514495659E06734310
chr31449573514495789E06734820
chr31449580614496177E06734891
chr31449622914496396E06735314
chr31449647314496537E06735558
chr31449657414496646E06735659
chr31449666014496814E06735745
chr31449686614496937E06735951
chr31449716814497364E06736253
chr31450214814502555E06741233
chr31450300014503054E06742085
chr31450310714503267E06742192
chr31450328714503532E06742372
chr31450360114503701E06742686
chr31441548014415562E068-45353
chr31441561914415834E068-45081
chr31441592814416126E068-44789
chr31443259514433182E068-27733
chr31445067814450783E068-10132
chr31445089914450958E068-9957
chr31445434114455584E068-5331
chr31445652714456796E068-4119
chr31445680014456872E068-4043
chr31445706414457333E068-3582
chr31445740014457551E068-3364
chr31445756214457804E068-3111
chr31445989514460091E068-824
chr31446687514467045E0685960
chr31446712614467185E0686211
chr31446738514467966E0686470
chr31446867714468727E0687762
chr31446873314468845E0687818
chr31446899014469057E0688075
chr31446933414469411E0688419
chr31446946214469524E0688547
chr31447235014472454E06811435
chr31447263614475032E06811721
chr31447520014476695E06814285
chr31447675914476847E06815844
chr31447695914477550E06816044
chr31447772214478031E06816807
chr31447814314478565E06817228
chr31448019114480247E06819276
chr31448030314480366E06819388
chr31448042014480478E06819505
chr31448061414480676E06819699
chr31448075714480851E06819842
chr31448088014481468E06819965
chr31448173814481949E06820823
chr31448204214482400E06821127
chr31448251914482866E06821604
chr31448305414483104E06822139
chr31448316414483347E06822249
chr31448335114483486E06822436
chr31448354714483698E06822632
chr31449031814490456E06829403
chr31449066814490807E06829753
chr31449086914491069E06829954
chr31449277414493110E06831859
chr31449318314493247E06832268
chr31449327614493453E06832361
chr31449346014495149E06832545
chr31449522514495659E06834310
chr31449573514495789E06834820
chr31449580614496177E06834891
chr31449622914496396E06835314
chr31449647314496537E06835558
chr31449657414496646E06835659
chr31449666014496814E06835745
chr31449686614496937E06835951
chr31449716814497364E06836253
chr31450162514501711E06840710
chr31450175214502058E06840837
chr31450214814502555E06841233
chr31450300014503054E06842085
chr31443259514433182E069-27733
chr31443319814433354E069-27561
chr31444680714446997E069-13918
chr31444791014447970E069-12945
chr31445434114455584E069-5331
chr31445652714456796E069-4119
chr31445680014456872E069-4043
chr31445706414457333E069-3582
chr31445740014457551E069-3364
chr31445756214457804E069-3111
chr31446966214470158E0698747
chr31447016114470211E0699246
chr31447030214470402E0699387
chr31447059614470646E0699681
chr31447081614471083E0699901
chr31447119414471332E06910279
chr31447235014472454E06911435
chr31447263614475032E06911721
chr31447520014476695E06914285
chr31447675914476847E06915844
chr31447695914477550E06916044
chr31447772214478031E06916807
chr31447814314478565E06917228
chr31448019114480247E06919276
chr31448030314480366E06919388
chr31448042014480478E06919505
chr31448061414480676E06919699
chr31448075714480851E06919842
chr31448088014481468E06919965
chr31448173814481949E06920823
chr31448204214482400E06921127
chr31448251914482866E06921604
chr31448305414483104E06922139
chr31448316414483347E06922249
chr31448335114483486E06922436
chr31448354714483698E06922632
chr31448379014483840E06922875
chr31448408814484138E06923173
chr31449031814490456E06929403
chr31449066814490807E06929753
chr31449086914491069E06929954
chr31449327614493453E06932361
chr31449346014495149E06932545
chr31449522514495659E06934310
chr31449573514495789E06934820
chr31449580614496177E06934891
chr31449622914496396E06935314
chr31449647314496537E06935558
chr31449657414496646E06935659
chr31449666014496814E06935745
chr31449686614496937E06935951
chr31450214814502555E06941233
chr31450300014503054E06942085
chr31450310714503267E06942192
chr31450328714503532E06942372
chr31450360114503701E06942686
chr31443758114437660E070-23255
chr31444680714446997E070-13918
chr31444705814447234E070-13681
chr31444739214447646E070-13269
chr31444791014447970E070-12945
chr31444802114448107E070-12808
chr31444815414448194E070-12721
chr31448019114480247E07019276
chr31448030314480366E07019388
chr31448042014480478E07019505
chr31448061414480676E07019699
chr31448075714480851E07019842
chr31448088014481468E07019965
chr31448173814481949E07020823
chr31448251914482866E07021604
chr31448305414483104E07022139
chr31448316414483347E07022249
chr31449327614493453E07032361
chr31449346014495149E07032545
chr31449716814497364E07036253
chr31444680714446997E071-13918
chr31444705814447234E071-13681
chr31444739214447646E071-13269
chr31444791014447970E071-12945
chr31444802114448107E071-12808
chr31444815414448194E071-12721
chr31445354814453748E071-7167
chr31445375814453840E071-7075
chr31445434114455584E071-5331
chr31445740014457551E071-3364
chr31445756214457804E071-3111
chr31445798114458058E071-2857
chr31445807514458166E071-2749
chr31446687514467045E0715960
chr31446873314468845E0717818
chr31446899014469057E0718075
chr31446933414469411E0718419
chr31446946214469524E0718547
chr31446966214470158E0718747
chr31447016114470211E0719246
chr31447030214470402E0719387
chr31447059614470646E0719681
chr31447081614471083E0719901
chr31447119414471332E07110279
chr31447136014471434E07110445
chr31447235014472454E07111435
chr31447263614475032E07111721
chr31447520014476695E07114285
chr31447772214478031E07116807
chr31447814314478565E07117228
chr31448019114480247E07119276
chr31448030314480366E07119388
chr31448042014480478E07119505
chr31448061414480676E07119699
chr31448075714480851E07119842
chr31448088014481468E07119965
chr31448173814481949E07120823
chr31448204214482400E07121127
chr31448251914482866E07121604
chr31448305414483104E07122139
chr31448316414483347E07122249
chr31448335114483486E07122436
chr31448354714483698E07122632
chr31449031814490456E07129403
chr31449066814490807E07129753
chr31449086914491069E07129954
chr31449327614493453E07132361
chr31449346014495149E07132545
chr31449522514495659E07134310
chr31449573514495789E07134820
chr31449580614496177E07134891
chr31449622914496396E07135314
chr31449647314496537E07135558
chr31449657414496646E07135659
chr31449666014496814E07135745
chr31449686614496937E07135951
chr31449716814497364E07136253
chr31449750514497574E07136590
chr31450175214502058E07140837
chr31450214814502555E07141233
chr31450300014503054E07142085
chr31450310714503267E07142192
chr31450328714503532E07142372
chr31450360114503701E07142686
chr31443259514433182E072-27733
chr31443319814433354E072-27561
chr31444680714446997E072-13918
chr31444705814447234E072-13681
chr31444739214447646E072-13269
chr31444791014447970E072-12945
chr31444802114448107E072-12808
chr31444815414448194E072-12721
chr31445434114455584E072-5331
chr31447059614470646E0729681
chr31447081614471083E0729901
chr31447235014472454E07211435
chr31447263614475032E07211721
chr31447520014476695E07214285
chr31447675914476847E07215844
chr31447695914477550E07216044
chr31447772214478031E07216807
chr31447814314478565E07217228
chr31448019114480247E07219276
chr31448030314480366E07219388
chr31448042014480478E07219505
chr31448061414480676E07219699
chr31448075714480851E07219842
chr31448088014481468E07219965
chr31448173814481949E07220823
chr31448204214482400E07221127
chr31448251914482866E07221604
chr31448305414483104E07222139
chr31448316414483347E07222249
chr31448335114483486E07222436
chr31448354714483698E07222632
chr31448379014483840E07222875
chr31448408814484138E07223173
chr31449031814490456E07229403
chr31449066814490807E07229753
chr31449086914491069E07229954
chr31449265514492740E07231740
chr31449277414493110E07231859
chr31449318314493247E07232268
chr31449327614493453E07232361
chr31449346014495149E07232545
chr31449522514495659E07234310
chr31449573514495789E07234820
chr31449580614496177E07234891
chr31449622914496396E07235314
chr31449657414496646E07235659
chr31449666014496814E07235745
chr31449686614496937E07235951
chr31449716814497364E07236253
chr31450175214502058E07240837
chr31450214814502555E07241233
chr31450300014503054E07242085
chr31450310714503267E07242192
chr31450328714503532E07242372
chr31451025514510305E07249340
chr31443259514433182E073-27733
chr31443319814433354E073-27561
chr31444739214447646E073-13269
chr31444791014447970E073-12945
chr31444802114448107E073-12808
chr31444815414448194E073-12721
chr31445434114455584E073-5331
chr31445652714456796E073-4119
chr31445680014456872E073-4043
chr31445706414457333E073-3582
chr31445740014457551E073-3364
chr31447030214470402E0739387
chr31447263614475032E07311721
chr31447520014476695E07314285
chr31447675914476847E07315844
chr31447695914477550E07316044
chr31447814314478565E07317228
chr31448019114480247E07319276
chr31448030314480366E07319388
chr31448042014480478E07319505
chr31448061414480676E07319699
chr31448075714480851E07319842
chr31448088014481468E07319965
chr31448173814481949E07320823
chr31448204214482400E07321127
chr31448251914482866E07321604
chr31448305414483104E07322139
chr31448316414483347E07322249
chr31448335114483486E07322436
chr31448354714483698E07322632
chr31449031814490456E07329403
chr31449346014495149E07332545
chr31449522514495659E07334310
chr31449573514495789E07334820
chr31449580614496177E07334891
chr31449622914496396E07335314
chr31449647314496537E07335558
chr31449657414496646E07335659
chr31450214814502555E07341233
chr31450300014503054E07342085
chr31450310714503267E07342192
chr31450328714503532E07342372
chr31450360114503701E07342686
chr31443259514433182E074-27733
chr31444680714446997E074-13918
chr31444705814447234E074-13681
chr31445434114455584E074-5331
chr31445652714456796E074-4119
chr31445680014456872E074-4043
chr31445706414457333E074-3582
chr31445740014457551E074-3364
chr31445756214457804E074-3111
chr31446933414469411E0748419
chr31446946214469524E0748547
chr31446966214470158E0748747
chr31447016114470211E0749246
chr31447030214470402E0749387
chr31447059614470646E0749681
chr31447081614471083E0749901
chr31447119414471332E07410279
chr31447136014471434E07410445
chr31447154814471708E07410633
chr31447175514471903E07410840
chr31447235014472454E07411435
chr31447263614475032E07411721
chr31447520014476695E07414285
chr31447675914476847E07415844
chr31447695914477550E07416044
chr31447772214478031E07416807
chr31447814314478565E07417228
chr31448019114480247E07419276
chr31448030314480366E07419388
chr31448042014480478E07419505
chr31448061414480676E07419699
chr31448075714480851E07419842
chr31448088014481468E07419965
chr31448173814481949E07420823
chr31448204214482400E07421127
chr31448251914482866E07421604
chr31448305414483104E07422139
chr31448316414483347E07422249
chr31448335114483486E07422436
chr31448354714483698E07422632
chr31448379014483840E07422875
chr31449031814490456E07429403
chr31449066814490807E07429753
chr31449086914491069E07429954
chr31449318314493247E07432268
chr31449327614493453E07432361
chr31449346014495149E07432545
chr31449522514495659E07434310
chr31449573514495789E07434820
chr31449580614496177E07434891
chr31449622914496396E07435314
chr31449647314496537E07435558
chr31449657414496646E07435659
chr31449666014496814E07435745
chr31449686614496937E07435951
chr31449716814497364E07436253
chr31450175214502058E07440837
chr31450214814502555E07441233
chr31450300014503054E07442085
chr31450310714503267E07442192
chr31450328714503532E07442372
chr31450360114503701E07442686
chr31450950714509817E07448592
chr31444680714446997E081-13918
chr31444705814447234E081-13681
chr31444739214447646E081-13269
chr31444791014447970E081-12945
chr31444802114448107E081-12808
chr31444815414448194E081-12721
chr31447520014476695E08114285
chr31447675914476847E08115844
chr31448019114480247E08119276
chr31448030314480366E08119388
chr31448042014480478E08119505
chr31448061414480676E08119699
chr31448075714480851E08119842
chr31448088014481468E08119965
chr31448173814481949E08120823
chr31448204214482400E08121127
chr31448251914482866E08121604
chr31448305414483104E08122139
chr31448316414483347E08122249
chr31449327614493453E08132361
chr31449346014495149E08132545
chr31449522514495659E08134310
chr31449573514495789E08134820
chr31449580614496177E08134891
chr31449622914496396E08135314
chr31449647314496537E08135558
chr31449657414496646E08135659
chr31449666014496814E08135745
chr31449686614496937E08135951
chr31449716814497364E08136253
chr31450214814502555E08141233
chr31447520014476695E08214285
chr31448019114480247E08219276
chr31448030314480366E08219388
chr31448042014480478E08219505
chr31448061414480676E08219699
chr31448075714480851E08219842
chr31448088014481468E08219965
chr31448251914482866E08221604
chr31449346014495149E08232545
chr31449522514495659E08234310
chr31449573514495789E08234820
chr31449580614496177E08234891
chr31449622914496396E08235314
chr31449647314496537E08235558
chr31449657414496646E08235659










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr31444312814444270E067-16645
chr31444312814444270E068-16645
chr31444312814444270E069-16645
chr31444312814444270E070-16645
chr31444312814444270E071-16645
chr31444312814444270E072-16645
chr31444312814444270E073-16645
chr31444312814444270E074-16645
chr31444312814444270E082-16645