rs8050990

Homo sapiens
C>T
LOC101927605 : Intron Variant
LOC729159 : 2KB Upstream Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0183 (5487/29928,GnomAD)
T=0201 (5863/29118,TOPMED)
T=0172 (859/5008,1000G)
T=0173 (666/3854,ALSPAC)
T=0176 (651/3708,TWINSUK)
chr16:60361443 (GRCh38.p7) (16q21)
AD
GWASdb2
1   publication(s)
See rs on genome
9 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 16NC_000016.10:g.60361443C>T
GRCh37.p13 chr 16NC_000016.9:g.60395347C>T

Gene: LOC729159, UPF0607 protein ENSP00000381418-like(minus strand): 2KB Upstream Variant

Molecule type Change Amino acid[Codon] SO Term
LOC729159 transcriptNM_001282301.1:c.N/AUpstream Transcript Variant

Gene: LOC101927605, uncharacterized LOC101927605(plus strand)

Molecule type Change Amino acid[Codon] SO Term
LOC101927605 transcript variant X1XR_001752229.1:n.N/AIntron Variant
LOC101927605 transcript variant X2XR_001752230.1:n.N/AIntron Variant
LOC101927605 transcript variant X3XR_001752231.1:n.N/AIntron Variant
LOC101927605 transcript variant X4XR_933654.2:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.724T=0.276
1000GenomesAmericanSub694C=0.870T=0.130
1000GenomesEast AsianSub1008C=0.898T=0.102
1000GenomesEuropeSub1006C=0.837T=0.163
1000GenomesGlobalStudy-wide5008C=0.828T=0.172
1000GenomesSouth AsianSub978C=0.860T=0.140
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.827T=0.173
The Genome Aggregation DatabaseAfricanSub8702C=0.748T=0.252
The Genome Aggregation DatabaseAmericanSub836C=0.890T=0.110
The Genome Aggregation DatabaseEast AsianSub1612C=0.919T=0.081
The Genome Aggregation DatabaseEuropeSub18476C=0.837T=0.162
The Genome Aggregation DatabaseGlobalStudy-wide29928C=0.816T=0.183
The Genome Aggregation DatabaseOtherSub302C=0.790T=0.210
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.798T=0.201
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.824T=0.176
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
rs80509900.0005alcohol dependence(early age of onset)20201924
rs80509900.00059alcohol dependence20201924

eQTL of rs8050990 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 rs8050990 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 )
chr166039564760395725E070300
chr166039584460395993E070497
chr166039730460397354E0701957
chr166039742560397498E0702078
chr166039756960397796E0702222
chr166041098360411092E07015636
chr166041111760411157E07015770
chr166039756960397796E0812222
chr166039756960397796E0822222