rs1000002

Homo sapiens
C>T
None
Check p-value
SNV (Single Nucleotide Variation)
T=0375 (11241/29936,GnomAD)
T=0344 (10042/29118,TOPMED)
T=0381 (1908/5008,1000G)
T=0482 (1856/3854,ALSPAC)
C==0498 (1847/3708,TWINSUK)
chr3:183917980 (GRCh38.p7) (3q27.1)
AD
GWASdb2
3   publication(s)
See rs on genome
20 Enhancers around
10 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 3NC_000003.12:g.183917980C>T
GRCh37.p13 chr 3NC_000003.11:g.183635768C>T

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.872T=0.128
1000GenomesAmericanSub694C=0.550T=0.450
1000GenomesEast AsianSub1008C=0.494T=0.506
1000GenomesEuropeSub1006C=0.520T=0.480
1000GenomesGlobalStudy-wide5008C=0.619T=0.381
1000GenomesSouth AsianSub978C=0.560T=0.440
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.518T=0.482
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.655T=0.344
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.498T=0.502
PMID Title Author Journal
21314694Genomewide association analysis of symptoms of alcohol dependence in the molecular genetics of schizophrenia (MGS2) control sample.Kendler KSAlcohol Clin Exp Res
18213362Multiplexed genotyping of ABC transporter polymorphisms with the Bioplex suspension array.Koo SHBiol Proced Online
19754948Evaluation of nine candidate genes in patients with normal tension glaucoma: a case control study.Wolf CBMC Med Genet

P-Value

SNP ID p-value Traits Study
rs10000020.000978alcohol dependence21314694

eQTL of rs1000002 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr3:183635768ABCC5ENSG00000114770.12C>T2.9062e-18-100035Cerebellum
Chr3:183635768ABCC5ENSG00000114770.12C>T3.8177e-4-100035Cortex
Chr3:183635768ABCC5ENSG00000114770.12C>T5.0692e-4-100035Hippocampus
Chr3:183635768ABCC5ENSG00000114770.12C>T6.5381e-3-100035Amygdala

meQTL of rs1000002 in Fetal Brain

Probe ID Position Gene beta p-value
cg01324343chr3:183735012ABCC50.1149883513784858.7026e-23
cg05044414chr3:183734942ABCC50.09836093375745751.5490e-18

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 )
chr3183600962183601026E067-34742
chr3183600962183601026E068-34742
chr3183600962183601026E069-34742
chr3183600962183601026E070-34742
chr3183600962183601026E071-34742
chr3183600962183601026E072-34742
chr3183613032183613428E072-22340
chr3183613471183613535E072-22233
chr3183600962183601026E073-34742
chr3183603378183603464E073-32304
chr3183603948183603999E073-31769
chr3183600962183601026E074-34742
chr3183600962183601026E081-34742
chr3183680476183680530E08144708
chr3183680574183681177E08144806
chr3183681502183681657E08145734
chr3183600962183601026E082-34742
chr3183680476183680530E08244708
chr3183680574183681177E08244806
chr3183681502183681657E08245734










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr3183601897183603221E067-32547
chr3183601897183603221E068-32547
chr3183601897183603221E069-32547
chr3183601897183603221E070-32547
chr3183601897183603221E071-32547
chr3183601897183603221E072-32547
chr3183601897183603221E073-32547
chr3183601897183603221E074-32547
chr3183601897183603221E081-32547
chr3183601897183603221E082-32547