rs2769490

Homo sapiens
T>C
LOC105370255 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T==0192 (5718/29774,GnomAD)
T==0207 (6046/29116,TOPMED)
T==0302 (1511/5008,1000G)
T==0140 (541/3854,ALSPAC)
T==0146 (543/3708,TWINSUK)
chr13:70794838 (GRCh38.p7) (13q21.33)
AD
GWASdb2
1   publication(s)
See rs on genome
3 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 13NC_000013.11:g.70794838T>C
GRCh37.p13 chr 13NC_000013.10:g.71368970T>C

Gene: LOC105370255, uncharacterized LOC105370255(plus strand)

Molecule type Change Amino acid[Codon] SO Term
LOC105370255 transcript variant X1XR_942058.2:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.259C=0.741
1000GenomesAmericanSub694T=0.190C=0.810
1000GenomesEast AsianSub1008T=0.533C=0.467
1000GenomesEuropeSub1006T=0.152C=0.848
1000GenomesGlobalStudy-wide5008T=0.302C=0.698
1000GenomesSouth AsianSub978T=0.360C=0.640
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.140C=0.860
The Genome Aggregation DatabaseAfricanSub8704T=0.234C=0.766
The Genome Aggregation DatabaseAmericanSub824T=0.220C=0.780
The Genome Aggregation DatabaseEast AsianSub1612T=0.532C=0.468
The Genome Aggregation DatabaseEuropeSub18332T=0.141C=0.858
The Genome Aggregation DatabaseGlobalStudy-wide29774T=0.192C=0.808
The Genome Aggregation DatabaseOtherSub302T=0.180C=0.820
Trans-Omics for Precision MedicineGlobalStudy-wide29116T=0.207C=0.792
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.146C=0.854
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
rs27694900.000343alcohol dependence20201924

eQTL of rs2769490 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 rs2769490 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 )
chr137132109471321144E081-47826
chr137132133771321387E081-47583
chr137132140571321679E081-47291