rs2394660

Homo sapiens
A>G
None
Check p-value
SNV (Single Nucleotide Variation)
A==0317 (9466/29854,GnomAD)
A==0293 (8559/29118,TOPMED)
A==0310 (1552/5008,1000G)
A==0284 (1093/3854,ALSPAC)
A==0279 (1033/3708,TWINSUK)
chr6:29704909 (GRCh38.p7) (6p22.1)
AD
GWASdb2
2   publication(s)
See rs on genome
50 Enhancers around
72 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 6NC_000006.12:g.29704909A>G
GRCh37.p13 chr 6NC_000006.11:g.29672686A>G
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_COX_CTG1NT_113891.3:g.1191427G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1NT_113891.2:g.1191533G>A
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_QBL_CTG1NT_167248.2:g.970408G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1NT_167248.1:g.976004G>A
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_DBB_CTG1NT_167245.2:g.970453G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1NT_167245.1:g.976038G>A
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1NT_167249.2:g.1013944A>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1NT_167249.1:g.1013242A>G
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_MANN_CTG1NT_167246.2:g.970022G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1NT_167246.1:g.975642G>A
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_MCF_CTG1NT_167247.2:g.970272G>A
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1NT_167247.1:g.975857G>A

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322A=0.311G=0.689
1000GenomesAmericanSub694A=0.270G=0.730
1000GenomesEast AsianSub1008A=0.309G=0.691
1000GenomesEuropeSub1006A=0.304G=0.696
1000GenomesGlobalStudy-wide5008A=0.310G=0.690
1000GenomesSouth AsianSub978A=0.350G=0.650
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.284G=0.716
The Genome Aggregation DatabaseAfricanSub8674A=0.316G=0.684
The Genome Aggregation DatabaseAmericanSub838A=0.290G=0.710
The Genome Aggregation DatabaseEast AsianSub1614A=0.341G=0.659
The Genome Aggregation DatabaseEuropeSub18426A=0.317G=0.682
The Genome Aggregation DatabaseGlobalStudy-wide29854A=0.317G=0.682
The Genome Aggregation DatabaseOtherSub302A=0.300G=0.700
Trans-Omics for Precision MedicineGlobalStudy-wide29118A=0.293G=0.706
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.279G=0.721
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
rs23946600.000846alcohol dependence20201924

eQTL of rs2394660 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr6:29672686RPL23AP1ENSG00000239257.1A>G3.1209e-7-21973Cerebellum
Chr6:29672686MICEENSG00000273340.1A>G7.2793e-10-40325Cerebellum
Chr6:29672686HLA-F-AS1ENSG00000214922.5A>G8.4756e-13-44084Cerebellum
Chr6:29672686HLA-HENSG00000206341.6A>G8.7137e-7-183558Cortex
Chr6:29672686MICEENSG00000273340.1A>G2.3222e-6-40325Cerebellar_Hemisphere
Chr6:29672686HLA-F-AS1ENSG00000214922.5A>G2.4717e-9-44084Cerebellar_Hemisphere
Chr6:29672686HLA-HENSG00000206341.6A>G2.5783e-22-183558Cerebellar_Hemisphere
Chr6:29672686HLA-HENSG00000206341.6A>G5.2793e-5-183558Caudate_basal_ganglia
Chr6:29672686HLA-KENSG00000230795.2A>G3.1711e-10-222269Hippocampus
Chr6:29672686HLA-KENSG00000230795.2A>G9.2361e-15-222269Nucleus_accumbens_basal_ganglia

meQTL of rs2394660 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 )
chr62962282629623241E067-49445
chr62962336229624255E067-48431
chr62963028929630395E067-42291
chr62963047929630577E067-42109
chr62963362729634063E067-38623
chr62963415729634383E067-38303
chr62969271529692823E06720029
chr62962282629623241E068-49445
chr62963362729634063E068-38623
chr62963415729634383E068-38303
chr62969380329694252E06821117
chr62962282629623241E069-49445
chr62962336229624255E069-48431
chr62963123129631471E069-41215
chr62963148829631807E069-40879
chr62963362729634063E069-38623
chr62963415729634383E069-38303
chr62963446629635320E069-37366
chr62969311229693419E06920426
chr62962282629623241E071-49445
chr62963148829631807E071-40879
chr62963187729631934E071-40752
chr62963231529632365E071-40321
chr62963362729634063E071-38623
chr62963415729634383E071-38303
chr62963446629635320E071-37366
chr62967022329670696E071-1990
chr62969311229693419E07120426
chr62969344129693782E07120755
chr62969380329694252E07121117
chr62972139829721522E07148712
chr62962336229624255E072-48431
chr62963123129631471E072-41215
chr62963148829631807E072-40879
chr62963187729631934E072-40752
chr62963362729634063E072-38623
chr62963415729634383E072-38303
chr62963446629635320E072-37366
chr62968070729680766E0728021
chr62969271529692823E07220029
chr62969311229693419E07220426
chr62969271529692823E07320029
chr62969311229693419E07320426
chr62962282629623241E074-49445
chr62962336229624255E074-48431
chr62963338429633535E074-39151
chr62963362729634063E074-38623
chr62963415729634383E074-38303
chr62963446629635320E074-37366
chr62963547529635581E074-37105







Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr62962499229625042E067-47644
chr62962600529626128E067-46558
chr62962768629627740E067-44946
chr62962935129629494E067-43192
chr62969068329691732E06717997
chr62969176029692347E06719074
chr62971613729717716E06743451
chr62971991229720033E06747226
chr62972005329720120E06747367
chr62972015629721181E06747470
chr62962499229625042E068-47644
chr62962600529626128E068-46558
chr62962768629627740E068-44946
chr62962935129629494E068-43192
chr62969068329691732E06817997
chr62969176029692347E06819074
chr62971613729717716E06843451
chr62971991229720033E06847226
chr62972005329720120E06847367
chr62972015629721181E06847470
chr62962499229625042E069-47644
chr62962600529626128E069-46558
chr62962768629627740E069-44946
chr62962935129629494E069-43192
chr62969068329691732E06917997
chr62969176029692347E06919074
chr62971613729717716E06943451
chr62971991229720033E06947226
chr62972005329720120E06947367
chr62972015629721181E06947470
chr62971991229720033E07047226
chr62972005329720120E07047367
chr62972015629721181E07047470
chr62962499229625042E071-47644
chr62962600529626128E071-46558
chr62962935129629494E071-43192
chr62969068329691732E07117997
chr62969176029692347E07119074
chr62971613729717716E07143451
chr62971991229720033E07147226
chr62972005329720120E07147367
chr62972015629721181E07147470
chr62962499229625042E072-47644
chr62962600529626128E072-46558
chr62962768629627740E072-44946
chr62969068329691732E07217997
chr62969176029692347E07219074
chr62971613729717716E07243451
chr62971991229720033E07247226
chr62972005329720120E07247367
chr62972015629721181E07247470
chr62962499229625042E073-47644
chr62962600529626128E073-46558
chr62962768629627740E073-44946
chr62969068329691732E07317997
chr62969176029692347E07319074
chr62971613729717716E07343451
chr62971991229720033E07347226
chr62972005329720120E07347367
chr62972015629721181E07347470
chr62962499229625042E074-47644
chr62962600529626128E074-46558
chr62962768629627740E074-44946
chr62962935129629494E074-43192
chr62969068329691732E07417997
chr62969176029692347E07419074
chr62971613729717716E07443451
chr62972015629721181E07447470
chr62969068329691732E08217997
chr62969176029692347E08219074
chr62971613729717716E08243451
chr62972015629721181E08247470