rs12905964

Homo sapiens
C>T
SH3GL3 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0432 (12929/29894,GnomAD)
C==0492 (14337/29118,TOPMED)
T=0448 (2244/5008,1000G)
T=0413 (1593/3854,ALSPAC)
T=0409 (1518/3708,TWINSUK)
chr15:83510363 (GRCh38.p7) (15q25.2)
AD
GWASdb2
1   publication(s)
See rs on genome
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 15NC_000015.10:g.83510363C>T
GRCh37.p13 chr 15NC_000015.9:g.84179115C>T

Gene: SH3GL3, SH3 domain containing GRB2 like 3(plus strand)

Molecule type Change Amino acid[Codon] SO Term
SH3GL3 transcript variant EEN-B2-L2NM_001301108.1:c.N/AIntron Variant
SH3GL3 transcript variant EEN-B2-L3NM_001301109.1:c.N/AIntron Variant
SH3GL3 transcript variant 5NM_001324182.1:c.N/AIntron Variant
SH3GL3 transcript variant 6NM_001324183.1:c.N/AIntron Variant
SH3GL3 transcript variant 7NM_001324184.1:c.N/AIntron Variant
SH3GL3 transcript variant 9NM_001324185.1:c.N/AIntron Variant
SH3GL3 transcript variant 13NM_001324186.1:c.N/AIntron Variant
SH3GL3 transcript variant 14NM_001324187.1:c.N/AIntron Variant
SH3GL3 transcript variant EEN-B2-L1NM_003027.4:c.N/AIntron Variant
SH3GL3 transcript variant 4NR_125370.1:n.N/AIntron Variant
SH3GL3 transcript variant 8NR_136711.1:n.N/AIntron Variant
SH3GL3 transcript variant 10NR_136712.1:n.N/AIntron Variant
SH3GL3 transcript variant 11NR_136713.1:n.N/AIntron Variant
SH3GL3 transcript variant 12NR_136714.1:n.N/AIntron Variant
SH3GL3 transcript variant X1XM_011521889.1:c.N/AIntron Variant
SH3GL3 transcript variant X11XM_011521891.2:c.N/AIntron Variant
SH3GL3 transcript variant X13XM_011521892.2:c.N/AIntron Variant
SH3GL3 transcript variant X6XM_017022486.1:c.N/AGenic Upstream Transcript Variant
SH3GL3 transcript variant X5XR_001751372.1:n.N/AIntron Variant
SH3GL3 transcript variant X7XR_001751373.1:n.N/AIntron Variant
SH3GL3 transcript variant X14XR_001751375.1:n.N/AIntron Variant
SH3GL3 transcript variant X2XR_931878.2:n.N/AIntron Variant
SH3GL3 transcript variant X3XR_931879.2:n.N/AIntron Variant
SH3GL3 transcript variant X4XR_931880.1:n.N/AIntron Variant
SH3GL3 transcript variant X9XR_931882.2:n.N/AIntron Variant
SH3GL3 transcript variant X8XR_001751374.1:n.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.396T=0.604
1000GenomesAmericanSub694C=0.350T=0.650
1000GenomesEast AsianSub1008C=0.505T=0.495
1000GenomesEuropeSub1006C=0.608T=0.392
1000GenomesGlobalStudy-wide5008C=0.552T=0.448
1000GenomesSouth AsianSub978C=0.900T=0.100
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.587T=0.413
The Genome Aggregation DatabaseAfricanSub8700C=0.420T=0.580
The Genome Aggregation DatabaseAmericanSub838C=0.330T=0.670
The Genome Aggregation DatabaseEast AsianSub1616C=0.512T=0.488
The Genome Aggregation DatabaseEuropeSub18438C=0.653T=0.346
The Genome Aggregation DatabaseGlobalStudy-wide29894C=0.567T=0.432
The Genome Aggregation DatabaseOtherSub302C=0.540T=0.460
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.492T=0.507
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.591T=0.409
PMID Title Author Journal
23743675A meta-analysis of two genome-wide association studies to identify novel loci for maximum number of alcoholic drinks.Kapoor MHum Genet

P-Value

SNP ID p-value Traits Study
rs129059648.63E-05alcohol consumption23743675

eQTL of rs12905964 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 rs12905964 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 )
chr158414019584140252E067-38863
chr158414038784140446E067-38669
chr158414173384141783E067-37332
chr158414295384143003E067-36112
chr158414321284143262E067-35853
chr158414336184143754E067-35361
chr158414401484144086E067-35029
chr158414432284144563E067-34552
chr158414478884144840E067-34275
chr158414495084145285E067-33830
chr158414545084146705E067-32410
chr158414674384146947E067-32168
chr158414697784147027E067-32088
chr158414811784148177E067-30938
chr158414824284148380E067-30735
chr158415705884157152E067-21963
chr158415739584157445E067-21670
chr158415768884157779E067-21336
chr158415797684158069E067-21046
chr158415979584159861E067-19254
chr158416025384160539E067-18576
chr158416146584161515E067-17600
chr158417767684177726E067-1389
chr158417795684178025E067-1090
chr158418098484181041E0671869
chr158418119184181597E0672076
chr158418164184181685E0672526
chr158418177584181835E0672660
chr158418187184181952E0672756
chr158418229584182345E0673180
chr158418355184183667E0674436
chr158418369084183740E0674575
chr158418397584184314E0674860
chr158420194884202149E06722833
chr158420243484202751E06723319
chr158420284384203196E06723728
chr158421807684218360E06738961
chr158421837184218878E06739256
chr158422700984227181E06747894
chr158422780584227845E06748690
chr158422801484228636E06748899
chr158422873084228780E06749615
chr158413090884131111E068-48004
chr158413116384131355E068-47760
chr158413138184131463E068-47652
chr158413173384132131E068-46984
chr158414336184143754E068-35361
chr158414545084146705E068-32410
chr158414674384146947E068-32168
chr158414697784147027E068-32088
chr158414710684147158E068-31957
chr158414719784147274E068-31841
chr158414742184147492E068-31623
chr158414811784148177E068-30938
chr158414824284148380E068-30735
chr158415003484150321E068-28794
chr158415033484150488E068-28627
chr158415052484150592E068-28523
chr158415637384156510E068-22605
chr158415705884157152E068-21963
chr158415739584157445E068-21670
chr158415768884157779E068-21336
chr158415797684158069E068-21046
chr158415979584159861E068-19254
chr158416025384160539E068-18576
chr158417514684175322E068-3793
chr158417767684177726E068-1389
chr158417795684178025E068-1090
chr158417886184179023E068-92
chr158418098484181041E0681869
chr158418119184181597E0682076
chr158418164184181685E0682526
chr158418177584181835E0682660
chr158418229584182345E0683180
chr158418355184183667E0684436
chr158418369084183740E0684575
chr158419020884190352E06811093
chr158419079384190843E06811678
chr158420144284201566E06822327
chr158420194884202149E06822833
chr158420469584204745E06825580
chr158421535184215541E06836236
chr158421807684218360E06838961
chr158421837184218878E06839256
chr158421895284219022E06839837
chr158422587584226013E06846760
chr158422637784226427E06847262
chr158422700984227181E06847894
chr158422780584227845E06848690
chr158413090884131111E069-48004
chr158413116384131355E069-47760
chr158413138184131463E069-47652
chr158413304184133091E069-46024
chr158414019584140252E069-38863
chr158414038784140446E069-38669
chr158414173384141783E069-37332
chr158414295384143003E069-36112
chr158414321284143262E069-35853
chr158414336184143754E069-35361
chr158414401484144086E069-35029
chr158414432284144563E069-34552
chr158414478884144840E069-34275
chr158414495084145285E069-33830
chr158414545084146705E069-32410
chr158414674384146947E069-32168
chr158414697784147027E069-32088
chr158414710684147158E069-31957
chr158414719784147274E069-31841
chr158414742184147492E069-31623
chr158414811784148177E069-30938
chr158414824284148380E069-30735
chr158415003484150321E069-28794
chr158415033484150488E069-28627
chr158415052484150592E069-28523
chr158415075084150800E069-28315
chr158415637384156510E069-22605
chr158415705884157152E069-21963
chr158415739584157445E069-21670
chr158415768884157779E069-21336
chr158415797684158069E069-21046
chr158415979584159861E069-19254
chr158416025384160539E069-18576
chr158416126084161381E069-17734
chr158416146584161515E069-17600
chr158416155784161621E069-17494
chr158417297484173035E069-6080
chr158417306184173547E069-5568
chr158417383584173894E069-5221
chr158417399984174049E069-5066
chr158417410484174154E069-4961
chr158417433984174389E069-4726
chr158417514684175322E069-3793
chr158417767684177726E069-1389
chr158417795684178025E069-1090
chr158417886184179023E069-92
chr158418098484181041E0691869
chr158418119184181597E0692076
chr158418355184183667E0694436
chr158418369084183740E0694575
chr158418397584184314E0694860
chr158418880984188869E0699694
chr158418889984188952E0699784
chr158418975884189808E06910643
chr158419020884190352E06911093
chr158419079384190843E06911678
chr158419098384191043E06911868
chr158419874684198800E06919631
chr158420243484202751E06923319
chr158420284384203196E06923728
chr158421497684215304E06935861
chr158421535184215541E06936236
chr158421807684218360E06938961
chr158421837184218878E06939256
chr158421895284219022E06939837
chr158422414984224226E06945034
chr158422454084224594E06945425
chr158422637784226427E06947262
chr158422700984227181E06947894
chr158422780584227845E06948690
chr158422801484228636E06948899
chr158422873084228780E06949615
chr158413138184131463E071-47652
chr158413173384132131E071-46984
chr158413304184133091E071-46024
chr158414019584140252E071-38863
chr158414038784140446E071-38669
chr158414173384141783E071-37332
chr158414295384143003E071-36112
chr158414321284143262E071-35853
chr158414336184143754E071-35361
chr158414401484144086E071-35029
chr158414432284144563E071-34552
chr158414478884144840E071-34275
chr158414495084145285E071-33830
chr158414545084146705E071-32410
chr158414674384146947E071-32168
chr158414742184147492E071-31623
chr158414811784148177E071-30938
chr158414824284148380E071-30735
chr158414841584148524E071-30591
chr158415075084150800E071-28315
chr158415637384156510E071-22605
chr158415705884157152E071-21963
chr158415739584157445E071-21670
chr158415768884157779E071-21336
chr158415797684158069E071-21046
chr158415979584159861E071-19254
chr158416025384160539E071-18576
chr158416126084161381E071-17734
chr158416146584161515E071-17600
chr158416155784161621E071-17494
chr158416262484162694E071-16421
chr158416869984168787E071-10328
chr158416880384168863E071-10252
chr158416890584168955E071-10160
chr158416923984169368E071-9747
chr158417247084172575E071-6540
chr158417276384172843E071-6272
chr158417297484173035E071-6080
chr158417306184173547E071-5568
chr158417767684177726E071-1389
chr158417795684178025E071-1090
chr158417886184179023E071-92
chr158418098484181041E0711869
chr158418119184181597E0712076
chr158418164184181685E0712526
chr158418177584181835E0712660
chr158418187184181952E0712756
chr158418229584182345E0713180
chr158418355184183667E0714436
chr158418369084183740E0714575
chr158418397584184314E0714860
chr158418579984185939E0716684
chr158418604584186095E0716930
chr158418708884187168E0717973
chr158418772984187791E0718614
chr158418880984188869E0719694
chr158418889984188952E0719784
chr158418975884189808E07110643
chr158419212984192179E07113014
chr158419225784192412E07113142
chr158419277284192906E07113657
chr158419874684198800E07119631
chr158420194884202149E07122833
chr158420243484202751E07123319
chr158420284384203196E07123728
chr158421468384214798E07135568
chr158421497684215304E07135861
chr158421535184215541E07136236
chr158421807684218360E07138961
chr158421837184218878E07139256
chr158421895284219022E07139837
chr158422007384220171E07140958
chr158422025684220315E07141141
chr158422032284220410E07141207
chr158422414984224226E07145034
chr158422454084224594E07145425
chr158422587584226013E07146760
chr158422637784226427E07147262
chr158422700984227181E07147894
chr158422780584227845E07148690
chr158422801484228636E07148899
chr158422873084228780E07149615
chr158413425584134335E072-44780
chr158414019584140252E072-38863
chr158414038784140446E072-38669
chr158414173384141783E072-37332
chr158414295384143003E072-36112
chr158414321284143262E072-35853
chr158414336184143754E072-35361
chr158414401484144086E072-35029
chr158414432284144563E072-34552
chr158414478884144840E072-34275
chr158414495084145285E072-33830
chr158414545084146705E072-32410
chr158414674384146947E072-32168
chr158414697784147027E072-32088
chr158414710684147158E072-31957
chr158414719784147274E072-31841
chr158414742184147492E072-31623
chr158414811784148177E072-30938
chr158414824284148380E072-30735
chr158414841584148524E072-30591
chr158414932084149446E072-29669
chr158415003484150321E072-28794
chr158415033484150488E072-28627
chr158415637384156510E072-22605
chr158415705884157152E072-21963
chr158415739584157445E072-21670
chr158415768884157779E072-21336
chr158415797684158069E072-21046
chr158415979584159861E072-19254
chr158416025384160539E072-18576
chr158416126084161381E072-17734
chr158417767684177726E072-1389
chr158417795684178025E072-1090
chr158417996284180092E072847
chr158418098484181041E0721869
chr158418119184181597E0722076
chr158418164184181685E0722526
chr158418177584181835E0722660
chr158418187184181952E0722756
chr158418229584182345E0723180
chr158418355184183667E0724436
chr158418369084183740E0724575
chr158418397584184314E0724860
chr158418708884187168E0727973
chr158418772984187791E0728614
chr158418880984188869E0729694
chr158418889984188952E0729784
chr158418975884189808E07210643
chr158419020884190352E07211093
chr158419079384190843E07211678
chr158419098384191043E07211868
chr158420194884202149E07222833
chr158420243484202751E07223319
chr158420284384203196E07223728
chr158421497684215304E07235861
chr158421535184215541E07236236
chr158422244184222573E07243326
chr158422414984224226E07245034
chr158422454084224594E07245425
chr158422565384225693E07246538
chr158422569984225749E07246584
chr158422587584226013E07246760
chr158422637784226427E07247262
chr158422700984227181E07247894
chr158422780584227845E07248690
chr158422801484228636E07248899
chr158414038784140446E073-38669
chr158414173384141783E073-37332
chr158414336184143754E073-35361
chr158414545084146705E073-32410
chr158414674384146947E073-32168
chr158414697784147027E073-32088
chr158414710684147158E073-31957
chr158414719784147274E073-31841
chr158414742184147492E073-31623
chr158415705884157152E073-21963
chr158415739584157445E073-21670
chr158415768884157779E073-21336
chr158415979584159861E073-19254
chr158416025384160539E073-18576
chr158417767684177726E073-1389
chr158417795684178025E073-1090
chr158422565384225693E07346538
chr158422569984225749E07346584
chr158422587584226013E07346760
chr158422637784226427E07347262
chr158422700984227181E07347894
chr158422780584227845E07348690
chr158413090884131111E074-48004
chr158413116384131355E074-47760
chr158413138184131463E074-47652
chr158414019584140252E074-38863
chr158414038784140446E074-38669
chr158414173384141783E074-37332
chr158414295384143003E074-36112
chr158414321284143262E074-35853
chr158414336184143754E074-35361
chr158414545084146705E074-32410
chr158414674384146947E074-32168
chr158414697784147027E074-32088
chr158414710684147158E074-31957
chr158414719784147274E074-31841
chr158414742184147492E074-31623
chr158414811784148177E074-30938
chr158414824284148380E074-30735
chr158415003484150321E074-28794
chr158415033484150488E074-28627
chr158415052484150592E074-28523
chr158415637384156510E074-22605
chr158415705884157152E074-21963
chr158415739584157445E074-21670
chr158415768884157779E074-21336
chr158415797684158069E074-21046
chr158415979584159861E074-19254
chr158416025384160539E074-18576
chr158416126084161381E074-17734
chr158416146584161515E074-17600
chr158416155784161621E074-17494
chr158416262484162694E074-16421
chr158416869984168787E074-10328
chr158417247084172575E074-6540
chr158417276384172843E074-6272
chr158417297484173035E074-6080
chr158417514684175322E074-3793
chr158417767684177726E074-1389
chr158417795684178025E074-1090
chr158418098484181041E0741869
chr158418119184181597E0742076
chr158419020884190352E07411093
chr158419079384190843E07411678
chr158419098384191043E07411868
chr158420194884202149E07422833
chr158420243484202751E07423319
chr158420284384203196E07423728
chr158420357284203649E07424457
chr158420580084206092E07426685
chr158421497684215304E07435861
chr158421535184215541E07436236
chr158421807684218360E07438961
chr158421837184218878E07439256
chr158421895284219022E07439837
chr158422414984224226E07445034
chr158422454084224594E07445425
chr158422487684224926E07445761
chr158422565384225693E07446538
chr158422569984225749E07446584
chr158422587584226013E07446760
chr158422637784226427E07447262
chr158422700984227181E07447894
chr158422780584227845E07448690
chr158414295384143003E081-36112
chr158414321284143262E081-35853
chr158414336184143754E081-35361
chr158414545084146705E081-32410
chr158414674384146947E081-32168
chr158414697784147027E081-32088
chr158414710684147158E081-31957
chr158414719784147274E081-31841
chr158415003484150321E081-28794
chr158415033484150488E081-28627
chr158420580084206092E08126685
chr158420616584206379E08127050
chr158420642884206652E08127313
chr158420666084206735E08127545
chr158420681484206868E08127699
chr158420693084207020E08127815
chr158420753584207691E08128420
chr158422007384220171E08140958
chr158422025684220315E08141141
chr158422032284220410E08141207
chr158422414984224226E08145034
chr158422454084224594E08145425
chr158414173384141783E082-37332
chr158414295384143003E082-36112
chr158414321284143262E082-35853
chr158414336184143754E082-35361
chr158414401484144086E082-35029
chr158414432284144563E082-34552
chr158414478884144840E082-34275
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chr158414545084146705E082-32410
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chr158414697784147027E082-32088
chr158414710684147158E082-31957
chr158414719784147274E082-31841
chr158415335584153960E082-25155
chr158421497684215304E08235861
chr158421535184215541E08236236
chr158421807684218360E08238961