rs17239999

Homo sapiens
C>T
GCOM1 : Intron Variant
MYZAP : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0215 (6468/29970,GnomAD)
T=0147 (735/5008,1000G)
T=0252 (973/3854,ALSPAC)
T=0257 (952/3708,TWINSUK)
chr15:57626376 (GRCh38.p7) (15q21.3)
AD
GWASdb2
1   publication(s)
See rs on genome
38 Enhancers around
8 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 15NC_000015.10:g.57626376C>T
GRCh37.p13 chr 15NC_000015.9:g.57918574C>T

Gene: GCOM1, GRINL1A complex locus 1(plus strand)

Molecule type Change Amino acid[Codon] SO Term
GCOM1 transcript variant 1NM_001018090.6:c.N/AIntron Variant
GCOM1 transcript variant 2NM_001018091.6:c.N/AIntron Variant
GCOM1 transcript variant 14NM_001285900.3:c.N/AIntron Variant
GCOM1 transcript variant 10NR_104367.2:n.N/AIntron Variant
GCOM1 transcript variant 3NR_104368.2:n.N/AIntron Variant
GCOM1 transcript variant 4NR_104369.2:n.N/AIntron Variant
GCOM1 transcript variant 5NR_104370.2:n.N/AIntron Variant
GCOM1 transcript variant 9NR_104371.3:n.N/AIntron Variant

Gene: MYZAP, myocardial zonula adherens protein(plus strand)

Molecule type Change Amino acid[Codon] SO Term
MYZAP transcript variant 1NM_001018100.4:c.N/AIntron Variant
MYZAP transcript variant 2NM_152451.7:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.900T=0.100
1000GenomesAmericanSub694C=0.850T=0.150
1000GenomesEast AsianSub1008C=0.932T=0.068
1000GenomesEuropeSub1006C=0.746T=0.254
1000GenomesGlobalStudy-wide5008C=0.853T=0.147
1000GenomesSouth AsianSub978C=0.830T=0.170
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.748T=0.252
The Genome Aggregation DatabaseAfricanSub8726C=0.875T=0.125
The Genome Aggregation DatabaseAmericanSub832C=0.820T=0.180
The Genome Aggregation DatabaseEast AsianSub1620C=0.921T=0.079
The Genome Aggregation DatabaseEuropeSub18490C=0.727T=0.272
The Genome Aggregation DatabaseGlobalStudy-wide29970C=0.784T=0.215
The Genome Aggregation DatabaseOtherSub302C=0.820T=0.180
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.743T=0.257
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
rs172399990.0008alcohol dependence20201924

eQTL of rs17239999 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 rs17239999 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 )
chr155791899557919271E067421
chr155788099057881070E068-37504
chr155788118357881273E068-37301
chr155788134457881423E068-37151
chr155791899557919271E068421
chr155789644757897249E069-21325
chr155793301257933062E06914438
chr155793309457933165E06914520
chr155794359757944076E06925023
chr155794425757944318E06925683
chr155791865757918798E07083
chr155791899557919271E070421
chr155792740157927490E0708827
chr155792757257928252E0708998
chr155788155357882255E071-36319
chr155788225657882367E071-36207
chr155789644757897249E071-21325
chr155794587757945927E07127303
chr155794359757944076E07225023
chr155794425757944318E07225683
chr155794521057945307E07226636
chr155789644757897249E073-21325
chr155788055857880944E074-37630
chr155788099057881070E074-37504
chr155788118357881273E074-37301
chr155788134457881423E074-37151
chr155791196257912302E074-6272
chr155791232757912407E074-6167
chr155791899557919271E074421
chr155793432557934412E07415751
chr155793448657934545E07415912
chr155792757257928252E0818998
chr155792716557927209E0828591
chr155792725657927365E0828682
chr155792740157927490E0828827
chr155792757257928252E0828998
chr155792846857928518E0829894
chr155792874457928794E08210170










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr155788335657885099E067-33475
chr155788335657885099E068-33475
chr155788335657885099E069-33475
chr155788335657885099E071-33475
chr155788335657885099E072-33475
chr155788335657885099E073-33475
chr155788335657885099E074-33475
chr155788335657885099E082-33475