rs1407662

Homo sapiens
A>G
LOC102724152 : Intron Variant
LOC107986666 : 2KB Upstream Variant
Check p-value
SNV (Single Nucleotide Variation)
A==0172 (5180/29958,GnomAD)
A==0179 (5229/29118,TOPMED)
A==0153 (767/5008,1000G)
A==0192 (740/3854,ALSPAC)
A==0192 (711/3708,TWINSUK)
chr6:163670625 (GRCh38.p7) (6q26)
AD
GWASdb2
1   publication(s)
See rs on genome
178 Enhancers around
1 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 6NC_000006.12:g.163670625A>G
GRCh37.p13 chr 6NC_000006.11:g.164091657A>G

Gene: LOC102724152, uncharacterized LOC102724152(minus strand)

Molecule type Change Amino acid[Codon] SO Term
LOC102724152 transcriptNR_134620.1:n.N/AIntron Variant

Gene: LOC107986666, uncharacterized LOC107986666(plus strand): 2KB Upstream Variant

Molecule type Change Amino acid[Codon] SO Term
LOC107986666 transcript variant X2XR_001744452.1:n.N/AUpstream Transcript Variant
LOC107986666 transcript variant X2XR_001744453.1:n.N/AUpstream Transcript Variant
LOC107986666 transcript variant X4XR_001744454.1:n.N/AUpstream Transcript Variant
LOC107986666 transcript variant X5XR_001744455.1:n.N/AUpstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322A=0.120G=0.880
1000GenomesAmericanSub694A=0.320G=0.680
1000GenomesEast AsianSub1008A=0.065G=0.935
1000GenomesEuropeSub1006A=0.157G=0.843
1000GenomesGlobalStudy-wide5008A=0.153G=0.847
1000GenomesSouth AsianSub978A=0.170G=0.830
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.192G=0.808
The Genome Aggregation DatabaseAfricanSub8726A=0.152G=0.848
The Genome Aggregation DatabaseAmericanSub838A=0.280G=0.720
The Genome Aggregation DatabaseEast AsianSub1622A=0.041G=0.959
The Genome Aggregation DatabaseEuropeSub18470A=0.189G=0.810
The Genome Aggregation DatabaseGlobalStudy-wide29958A=0.172G=0.827
The Genome Aggregation DatabaseOtherSub302A=0.160G=0.840
Trans-Omics for Precision MedicineGlobalStudy-wide29118A=0.179G=0.820
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.192G=0.808
PMID Title Author Journal
20201924Genome-wide association study of alcohol dependence implicates a region on chromosome 11.Edenberg HJAlcohol Clin Exp Res

P-Value

SNP ID p-value Traits Study
rs14076620.00027alcohol dependence20201924

eQTL of rs1407662 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 rs1407662 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 )
chr6164082265164082726E067-8931
chr6164082935164082985E067-8672
chr6164082986164083038E067-8619
chr6164087960164088019E067-3638
chr6164088095164088145E067-3512
chr6164088209164088486E067-3171
chr6164088582164089384E067-2273
chr6164090815164090877E067-780
chr6164109935164110272E06718278
chr6164110779164110854E06719122
chr6164128386164128850E06736729
chr6164128893164129298E06737236
chr6164130096164130378E06738439
chr6164130381164130535E06738724
chr6164131012164133959E06739355
chr6164134110164134305E06742453
chr6164073032164073334E068-18323
chr6164073337164073609E068-18048
chr6164082150164082242E068-9415
chr6164082265164082726E068-8931
chr6164082935164082985E068-8672
chr6164082986164083038E068-8619
chr6164087960164088019E068-3638
chr6164088095164088145E068-3512
chr6164088209164088486E068-3171
chr6164088582164089384E068-2273
chr6164109935164110272E06818278
chr6164110779164110854E06819122
chr6164110969164111088E06819312
chr6164127845164128009E06836188
chr6164128386164128850E06836729
chr6164130381164130535E06838724
chr6164130775164130957E06839118
chr6164131012164133959E06839355
chr6164134110164134305E06842453
chr6164138421164139004E06846764
chr6164082265164082726E069-8931
chr6164082935164082985E069-8672
chr6164082986164083038E069-8619
chr6164087960164088019E069-3638
chr6164088095164088145E069-3512
chr6164088209164088486E069-3171
chr6164088582164089384E069-2273
chr6164089410164089722E069-1935
chr6164109935164110272E06918278
chr6164110779164110854E06919122
chr6164110969164111088E06919312
chr6164128386164128850E06936729
chr6164128893164129298E06937236
chr6164129350164129512E06937693
chr6164129532164129611E06937875
chr6164130096164130378E06938439
chr6164130381164130535E06938724
chr6164130627164130733E06938970
chr6164130775164130957E06939118
chr6164131012164133959E06939355
chr6164140138164140188E06948481
chr6164141212164141310E06949555
chr6164141339164141440E06949682
chr6164056805164057274E070-34383
chr6164073032164073334E070-18323
chr6164073337164073609E070-18048
chr6164073855164073905E070-17752
chr6164073926164073992E070-17665
chr6164082265164082726E070-8931
chr6164082935164082985E070-8672
chr6164082986164083038E070-8619
chr6164085763164085813E070-5844
chr6164086313164086386E070-5271
chr6164086946164086996E070-4661
chr6164087059164087339E070-4318
chr6164087489164087616E070-4041
chr6164087960164088019E070-3638
chr6164088095164088145E070-3512
chr6164088209164088486E070-3171
chr6164088582164089384E070-2273
chr6164089410164089722E070-1935
chr6164090815164090877E070-780
chr6164091272164091666E0700
chr6164128386164128850E07036729
chr6164128893164129298E07037236
chr6164139085164139259E07047428
chr6164139398164139525E07047741
chr6164139601164139663E07047944
chr6164139719164139851E07048062
chr6164139920164140027E07048263
chr6164140138164140188E07048481
chr6164140353164140633E07048696
chr6164073032164073334E071-18323
chr6164073337164073609E071-18048
chr6164081625164081727E071-9930
chr6164082150164082242E071-9415
chr6164082265164082726E071-8931
chr6164082935164082985E071-8672
chr6164082986164083038E071-8619
chr6164087960164088019E071-3638
chr6164088095164088145E071-3512
chr6164088209164088486E071-3171
chr6164088582164089384E071-2273
chr6164089410164089722E071-1935
chr6164109935164110272E07118278
chr6164110779164110854E07119122
chr6164110969164111088E07119312
chr6164122413164122463E07130756
chr6164122637164122718E07130980
chr6164123222164123282E07131565
chr6164126606164126656E07134949
chr6164126755164126814E07135098
chr6164127039164127124E07135382
chr6164127299164127366E07135642
chr6164128386164128850E07136729
chr6164128893164129298E07137236
chr6164129350164129512E07137693
chr6164130381164130535E07138724
chr6164130627164130733E07138970
chr6164130775164130957E07139118
chr6164131012164133959E07139355
chr6164134110164134305E07142453
chr6164073032164073334E072-18323
chr6164082150164082242E072-9415
chr6164082265164082726E072-8931
chr6164082935164082985E072-8672
chr6164082986164083038E072-8619
chr6164088582164089384E072-2273
chr6164109935164110272E07218278
chr6164110969164111088E07219312
chr6164128386164128850E07236729
chr6164128893164129298E07237236
chr6164134110164134305E07242453
chr6164088095164088145E073-3512
chr6164088582164089384E073-2273
chr6164089410164089722E073-1935
chr6164109935164110272E07318278
chr6164127299164127366E07335642
chr6164128893164129298E07337236
chr6164129350164129512E07337693
chr6164129532164129611E07337875
chr6164130775164130957E07339118
chr6164131012164133959E07339355
chr6164134110164134305E07342453
chr6164082150164082242E074-9415
chr6164082265164082726E074-8931
chr6164082935164082985E074-8672
chr6164082986164083038E074-8619
chr6164083433164083589E074-8068
chr6164083702164083752E074-7905
chr6164087960164088019E074-3638
chr6164088095164088145E074-3512
chr6164088209164088486E074-3171
chr6164088582164089384E074-2273
chr6164109935164110272E07418278
chr6164110779164110854E07419122
chr6164110969164111088E07419312
chr6164130775164130957E07439118
chr6164131012164133959E07439355
chr6164134110164134305E07442453
chr6164141212164141310E07449555
chr6164141339164141440E07449682
chr6164073032164073334E081-18323
chr6164073337164073609E081-18048
chr6164073855164073905E081-17752
chr6164073926164073992E081-17665
chr6164086313164086386E081-5271
chr6164086946164086996E081-4661
chr6164087059164087339E081-4318
chr6164087489164087616E081-4041
chr6164087960164088019E081-3638
chr6164088095164088145E081-3512
chr6164088209164088486E081-3171
chr6164088582164089384E081-2273
chr6164089410164089722E081-1935
chr6164107182164107295E08115525
chr6164107462164107570E08115805
chr6164107598164107738E08115941
chr6164107964164108031E08116307
chr6164139601164139663E08247944
chr6164141212164141310E08249555
chr6164141339164141440E08249682










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr6164099133164099270E0707476