rs3129985

Homo sapiens
C>T
None
Check p-value
SNV (Single Nucleotide Variation)
T=0087 (2636/29974,GnomAD)
T=0083 (2438/29118,TOPMED)
T=0037 (183/5008,1000G)
T=0155 (599/3854,ALSPAC)
T=0159 (589/3708,TWINSUK)
chr6:30794765 (GRCh38.p7) (6p21.33)
AD
GWASdb2
1   publication(s)
See rs on genome
102 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 6NC_000006.12:g.30794765C>T
GRCh37.p13 chr 6NC_000006.11:g.30762542C>T
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_COX_CTG1NT_113891.3:g.2274482T>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1NT_113891.2:g.2274588T>C
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_QBL_CTG1NT_167248.2:g.2049849C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1NT_167248.1:g.2055445C>T
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_DBB_CTG1NT_167245.2:g.2051044C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1NT_167245.1:g.2056629C>T
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1NT_167249.2:g.2095525C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1NT_167249.1:g.2094823C>T
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_MANN_CTG1NT_167246.2:g.2105007C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1NT_167246.1:g.2110627C>T

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.964T=0.036
1000GenomesAmericanSub694C=0.960T=0.040
1000GenomesEast AsianSub1008C=0.997T=0.003
1000GenomesEuropeSub1006C=0.907T=0.093
1000GenomesGlobalStudy-wide5008C=0.963T=0.037
1000GenomesSouth AsianSub978C=0.990T=0.010
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.845T=0.155
The Genome Aggregation DatabaseAfricanSub8726C=0.950T=0.050
The Genome Aggregation DatabaseAmericanSub838C=0.970T=0.030
The Genome Aggregation DatabaseEast AsianSub1622C=0.999T=0.001
The Genome Aggregation DatabaseEuropeSub18486C=0.883T=0.116
The Genome Aggregation DatabaseGlobalStudy-wide29974C=0.912T=0.087
The Genome Aggregation DatabaseOtherSub302C=0.920T=0.080
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.916T=0.083
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.841T=0.159
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
rs31299850.00099alcohol dependence20201924

eQTL of rs3129985 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr6:30762542HLA-KENSG00000230795.2C>T4.6103e-20867587Cerebellum
Chr6:30762542FLOT1ENSG00000137312.10C>T1.2158e-652032Cerebellum
Chr6:30762542CCHCR1ENSG00000204536.9C>T1.0258e-9-363473Cerebellum
Chr6:30762542MICBENSG00000204516.5C>T0.0000e+0-700116Cerebellum
Chr6:30762542HLA-KENSG00000230795.2C>T1.0204e-14867587Frontal_Cortex_BA9
Chr6:30762542HLA-KENSG00000230795.2C>T3.2193e-14867587Cortex
Chr6:30762542HLA-KENSG00000230795.2C>T1.9542e-17867587Cerebellar_Hemisphere
Chr6:30762542CCHCR1ENSG00000204536.9C>T6.3052e-8-363473Cerebellar_Hemisphere
Chr6:30762542MICBENSG00000204516.5C>T1.7000e-27-700116Cerebellar_Hemisphere
Chr6:30762542VARS2ENSG00000137411.12C>T6.3004e-11-119440Hippocampus
Chr6:30762542HLA-KENSG00000230795.2C>T9.2361e-15867587Nucleus_accumbens_basal_ganglia

meQTL of rs3129985 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 )
chr63071929030719432E067-43110
chr63073642730736602E067-25940
chr63074876230748894E067-13648
chr63078970330790554E06727161
chr63079565030795984E06733108
chr63079598630796967E06733444
chr63080566730805807E06743125
chr63080589730806033E06743355
chr63080618930806548E06743647
chr63071929030719432E068-43110
chr63071949330720797E068-41745
chr63073127330732396E068-30146
chr63073642730736602E068-25940
chr63073663930738260E068-24282
chr63074584930746367E068-16175
chr63074641630746774E068-15768
chr63074687230746955E068-15587
chr63074703730747720E068-14822
chr63074777630748277E068-14265
chr63074876230748894E068-13648
chr63078970330790554E06827161
chr63079565030795984E06833108
chr63079598630796967E06833444
chr63071949330720797E069-41745
chr63073642730736602E069-25940
chr63074876230748894E069-13648
chr63079565030795984E06933108
chr63079598630796967E06933444
chr63071285230712973E070-49569
chr63071301830713177E070-49365
chr63071320030713296E070-49246
chr63071336530713429E070-49113
chr63074703730747720E070-14822
chr63074876230748894E070-13648
chr63080425130804471E07041709
chr63080490430804958E07042362
chr63080566730805807E07043125
chr63080589730806033E07043355
chr63080618930806548E07043647
chr63071949330720797E071-41745
chr63072082330720890E071-41652
chr63072097630721065E071-41477
chr63072383530723889E071-38653
chr63073127330732396E071-30146
chr63073642730736602E071-25940
chr63073663930738260E071-24282
chr63074584930746367E071-16175
chr63074641630746774E071-15768
chr63074703730747720E071-14822
chr63074777630748277E071-14265
chr63074847030748731E071-13811
chr63074876230748894E071-13648
chr63078970330790554E07127161
chr63079056730790758E07128025
chr63079565030795984E07133108
chr63079598630796967E07133444
chr63080566730805807E07143125
chr63073127330732396E072-30146
chr63073663930738260E072-24282
chr63074777630748277E072-14265
chr63074876230748894E072-13648
chr63074917330750706E072-11836
chr63078970330790554E07227161
chr63079565030795984E07233108
chr63079598630796967E07233444
chr63073127330732396E073-30146
chr63073423130734643E073-27899
chr63073642730736602E073-25940
chr63073663930738260E073-24282
chr63074641630746774E073-15768
chr63074687230746955E073-15587
chr63074703730747720E073-14822
chr63074777630748277E073-14265
chr63074847030748731E073-13811
chr63074876230748894E073-13648
chr63079565030795984E07333108
chr63079598630796967E07333444
chr63071949330720797E074-41745
chr63073127330732396E074-30146
chr63074444330744515E074-18027
chr63074584930746367E074-16175
chr63074641630746774E074-15768
chr63074777630748277E074-14265
chr63074876230748894E074-13648
chr63074917330750706E074-11836
chr63076620630766278E0743664
chr63076631230766548E0743770
chr63076656930766867E0744027
chr63078970330790554E07427161
chr63079056730790758E07428025
chr63079565030795984E07433108
chr63079598630796967E07433444
chr63080566730805807E07443125
chr63080589730806033E07443355
chr63080618930806548E07443647
chr63080662130806671E07444079
chr63071285230712973E081-49569
chr63074847030748731E081-13811
chr63074876230748894E081-13648
chr63074847030748731E082-13811
chr63074876230748894E082-13648
chr63074917330750706E082-11836