rs3131863

Homo sapiens
G>A
None
Check p-value
SNV (Single Nucleotide Variation)
G==0317 (9490/29914,GnomAD)
G==0293 (8558/29118,TOPMED)
G==0310 (1554/5008,1000G)
G==0283 (1092/3854,ALSPAC)
G==0278 (1030/3708,TWINSUK)
chr6:29705706 (GRCh38.p7) (6p22.1)
AD
GWASdb2
2   publication(s)
See rs on genome
41 Enhancers around
72 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 6NC_000006.12:g.29705706G>A
GRCh37.p13 chr 6NC_000006.11:g.29673483G>A
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_COX_CTG1NT_113891.3:g.1192225A>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1NT_113891.2:g.1192331A>G
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_QBL_CTG1NT_167248.2:g.971206A>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1NT_167248.1:g.976802A>G
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_DBB_CTG1NT_167245.2:g.971251A>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1NT_167245.1:g.976836A>G
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1NT_167249.2:g.1014741G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1NT_167249.1:g.1014039G>A
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_MANN_CTG1NT_167246.2:g.970820A>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1NT_167246.1:g.976440A>G
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_MCF_CTG1NT_167247.2:g.971070A>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1NT_167247.1:g.976655A>G

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.312A=0.688
1000GenomesAmericanSub694G=0.270A=0.730
1000GenomesEast AsianSub1008G=0.309A=0.691
1000GenomesEuropeSub1006G=0.304A=0.696
1000GenomesGlobalStudy-wide5008G=0.310A=0.690
1000GenomesSouth AsianSub978G=0.350A=0.650
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.283A=0.717
The Genome Aggregation DatabaseAfricanSub8704G=0.317A=0.683
The Genome Aggregation DatabaseAmericanSub838G=0.290A=0.710
The Genome Aggregation DatabaseEast AsianSub1608G=0.340A=0.660
The Genome Aggregation DatabaseEuropeSub18462G=0.317A=0.682
The Genome Aggregation DatabaseGlobalStudy-wide29914G=0.317A=0.682
The Genome Aggregation DatabaseOtherSub302G=0.300A=0.700
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.293A=0.706
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.278A=0.722
PMID Title Author Journal
20201924Genome-wide association study of alcohol dependence implicates a region on chromosome 11.Edenberg HJAlcohol Clin Exp Res
27766139Methodology for single nucleotide polymorphism selection in promoter regions for clinical use. An example of its applicability.Marques HInt J Mol Epidemiol Genet

P-Value

SNP ID p-value Traits Study
rs31318630.000845alcohol dependence20201924

eQTL of rs3131863 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr6:29673483RPL23AP1ENSG00000239257.1G>A3.1209e-7-21176Cerebellum
Chr6:29673483MICEENSG00000273340.1G>A7.2793e-10-39528Cerebellum
Chr6:29673483HLA-F-AS1ENSG00000214922.5G>A8.4756e-13-43287Cerebellum
Chr6:29673483HLA-HENSG00000206341.6G>A8.7137e-7-182761Cortex
Chr6:29673483MICEENSG00000273340.1G>A2.3222e-6-39528Cerebellar_Hemisphere
Chr6:29673483HLA-F-AS1ENSG00000214922.5G>A2.4717e-9-43287Cerebellar_Hemisphere
Chr6:29673483HLA-HENSG00000206341.6G>A2.5783e-22-182761Cerebellar_Hemisphere
Chr6:29673483HLA-HENSG00000206341.6G>A5.2793e-5-182761Caudate_basal_ganglia
Chr6:29673483HLA-KENSG00000230795.2G>A3.1711e-10-221472Hippocampus
Chr6:29673483HLA-KENSG00000230795.2G>A9.2361e-15-221472Nucleus_accumbens_basal_ganglia

meQTL of rs3131863 in Fetal Brain

Probe ID Position Gene beta p-value
cg22298860chr6:29690822HLA-F-0.07104277367772279.6047e-21
cg04186657chr6:29690893HLA-F-0.08220530931167311.5051e-13
cg11201654chr6:29690766HLA-F-0.08407446089837875.3821e-13
cg11768167chr6:29690889HLA-F-0.06891833114609111.7921e-12
cg21114334chr6:29720137IFITM4P-0.04765927628648322.9721e-9

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 )
chr62963028929630395E067-43088
chr62963047929630577E067-42906
chr62963362729634063E067-39420
chr62963415729634383E067-39100
chr62969271529692823E06719232
chr62963362729634063E068-39420
chr62963415729634383E068-39100
chr62969380329694252E06820320
chr62963123129631471E069-42012
chr62963148829631807E069-41676
chr62963362729634063E069-39420
chr62963415729634383E069-39100
chr62963446629635320E069-38163
chr62969311229693419E06919629
chr62963148829631807E071-41676
chr62963187729631934E071-41549
chr62963231529632365E071-41118
chr62963362729634063E071-39420
chr62963415729634383E071-39100
chr62963446629635320E071-38163
chr62967022329670696E071-2787
chr62969311229693419E07119629
chr62969344129693782E07119958
chr62969380329694252E07120320
chr62972139829721522E07147915
chr62963123129631471E072-42012
chr62963148829631807E072-41676
chr62963187729631934E072-41549
chr62963362729634063E072-39420
chr62963415729634383E072-39100
chr62963446629635320E072-38163
chr62968070729680766E0727224
chr62969271529692823E07219232
chr62969311229693419E07219629
chr62969271529692823E07319232
chr62969311229693419E07319629
chr62963338429633535E074-39948
chr62963362729634063E074-39420
chr62963415729634383E074-39100
chr62963446629635320E074-38163
chr62963547529635581E074-37902







Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr62962499229625042E067-48441
chr62962600529626128E067-47355
chr62962768629627740E067-45743
chr62962935129629494E067-43989
chr62969068329691732E06717200
chr62969176029692347E06718277
chr62971613729717716E06742654
chr62971991229720033E06746429
chr62972005329720120E06746570
chr62972015629721181E06746673
chr62962499229625042E068-48441
chr62962600529626128E068-47355
chr62962768629627740E068-45743
chr62962935129629494E068-43989
chr62969068329691732E06817200
chr62969176029692347E06818277
chr62971613729717716E06842654
chr62971991229720033E06846429
chr62972005329720120E06846570
chr62972015629721181E06846673
chr62962499229625042E069-48441
chr62962600529626128E069-47355
chr62962768629627740E069-45743
chr62962935129629494E069-43989
chr62969068329691732E06917200
chr62969176029692347E06918277
chr62971613729717716E06942654
chr62971991229720033E06946429
chr62972005329720120E06946570
chr62972015629721181E06946673
chr62971991229720033E07046429
chr62972005329720120E07046570
chr62972015629721181E07046673
chr62962499229625042E071-48441
chr62962600529626128E071-47355
chr62962935129629494E071-43989
chr62969068329691732E07117200
chr62969176029692347E07118277
chr62971613729717716E07142654
chr62971991229720033E07146429
chr62972005329720120E07146570
chr62972015629721181E07146673
chr62962499229625042E072-48441
chr62962600529626128E072-47355
chr62962768629627740E072-45743
chr62969068329691732E07217200
chr62969176029692347E07218277
chr62971613729717716E07242654
chr62971991229720033E07246429
chr62972005329720120E07246570
chr62972015629721181E07246673
chr62962499229625042E073-48441
chr62962600529626128E073-47355
chr62962768629627740E073-45743
chr62969068329691732E07317200
chr62969176029692347E07318277
chr62971613729717716E07342654
chr62971991229720033E07346429
chr62972005329720120E07346570
chr62972015629721181E07346673
chr62962499229625042E074-48441
chr62962600529626128E074-47355
chr62962768629627740E074-45743
chr62962935129629494E074-43989
chr62969068329691732E07417200
chr62969176029692347E07418277
chr62971613729717716E07442654
chr62972015629721181E07446673
chr62969068329691732E08217200
chr62969176029692347E08218277
chr62971613729717716E08242654
chr62972015629721181E08246673