rs959781

Homo sapiens
C>T
LOC105378305 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C==0112 (3359/29944,GnomAD)
C==0150 (4375/29118,TOPMED)
C==0133 (666/5008,1000G)
C==0086 (331/3854,ALSPAC)
C==0094 (348/3708,TWINSUK)
chr10:52640042 (GRCh38.p7) (10q21.1)
AD
GWASdb2
1   publication(s)
See rs on genome
58 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 10NC_000010.11:g.52640042C>T
GRCh37.p13 chr 10NC_000010.10:g.54399802C>T

Gene: LOC105378305, uncharacterized LOC105378305(minus strand)

Molecule type Change Amino acid[Codon] SO Term
LOC105378305 transcript variant X2XR_945961.2:n.N/AIntron Variant
LOC105378305 transcript variant X1XR_945962.2:n.N/AIntron Variant
LOC105378305 transcript variant X3XR_001747449.1:n.N/AGenic Upstream Transcript Variant
LOC105378305 transcript variant X4XR_001747450.1:n.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.234T=0.766
1000GenomesAmericanSub694C=0.170T=0.830
1000GenomesEast AsianSub1008C=0.052T=0.948
1000GenomesEuropeSub1006C=0.107T=0.893
1000GenomesGlobalStudy-wide5008C=0.133T=0.867
1000GenomesSouth AsianSub978C=0.080T=0.920
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.086T=0.914
The Genome Aggregation DatabaseAfricanSub8722C=0.194T=0.806
The Genome Aggregation DatabaseAmericanSub836C=0.250T=0.750
The Genome Aggregation DatabaseEast AsianSub1614C=0.056T=0.944
The Genome Aggregation DatabaseEuropeSub18472C=0.071T=0.928
The Genome Aggregation DatabaseGlobalStudy-wide29944C=0.112T=0.887
The Genome Aggregation DatabaseOtherSub300C=0.150T=0.850
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.150T=0.849
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.094T=0.906
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
rs9597810.000167alcohol dependence20201924

eQTL of rs959781 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 rs959781 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 )
chr105440432154404451E0674519
chr105440448954404792E0674687
chr105440508054405330E0675278
chr105440533854405547E0675536
chr105441072454410815E06710922
chr105441084454410925E06711042
chr105441113154411319E06711329
chr105441135554411482E06711553
chr105441216754413132E06712365
chr105441326454413611E06713462
chr105441393954414436E06714137
chr105440508054405330E0685278
chr105440533854405547E0685536
chr105441113154411319E06811329
chr105441135554411482E06811553
chr105441216754413132E06812365
chr105438823154388461E069-11341
chr105440432154404451E0694519
chr105440448954404792E0694687
chr105440508054405330E0695278
chr105440533854405547E0695536
chr105441072454410815E06910922
chr105441084454410925E06911042
chr105441113154411319E06911329
chr105441135554411482E06911553
chr105441216754413132E06912365
chr105440448954404792E0704687
chr105440508054405330E0705278
chr105441113154411319E07011329
chr105441135554411482E07011553
chr105440508054405330E0715278
chr105440533854405547E0715536
chr105441072454410815E07110922
chr105441084454410925E07111042
chr105441113154411319E07111329
chr105441135554411482E07111553
chr105441326454413611E07113462
chr105438823154388461E072-11341
chr105440448954404792E0724687
chr105440508054405330E0725278
chr105440533854405547E0725536
chr105441113154411319E07211329
chr105441135554411482E07211553
chr105441216754413132E07212365
chr105441326454413611E07213462
chr105441113154411319E07311329
chr105441135554411482E07311553
chr105441216754413132E07312365
chr105438823154388461E074-11341
chr105440508054405330E0745278
chr105440533854405547E0745536
chr105441072454410815E07410922
chr105441084454410925E07411042
chr105441113154411319E07411329
chr105441135554411482E07411553
chr105441216754413132E07412365
chr105441326454413611E07413462
chr105441393954414436E07414137