rs838530

Homo sapiens
T>C
LOC105378934 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0208 (6236/29972,GnomAD)
C=0284 (8285/29118,TOPMED)
C=0283 (1415/5008,1000G)
C=0062 (240/3854,ALSPAC)
C=0067 (249/3708,TWINSUK)
chr1:119354876 (GRCh38.p7) (1p12)
AD
GWASdb2
1   publication(s)
See rs on genome
11 Enhancers around
9 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 1NC_000001.11:g.119354876T>C
GRCh37.p13 chr 1NC_000001.10:g.119897499T>C

Gene: LOC105378934, uncharacterized LOC105378934(plus strand)

Molecule type Change Amino acid[Codon] SO Term
LOC105378934 transcriptXR_947752.2:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.393C=0.607
1000GenomesAmericanSub694T=0.860C=0.140
1000GenomesEast AsianSub1008T=0.754C=0.246
1000GenomesEuropeSub1006T=0.935C=0.065
1000GenomesGlobalStudy-wide5008T=0.717C=0.283
1000GenomesSouth AsianSub978T=0.790C=0.210
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.938C=0.062
The Genome Aggregation DatabaseAfricanSub8716T=0.466C=0.534
The Genome Aggregation DatabaseAmericanSub838T=0.870C=0.130
The Genome Aggregation DatabaseEast AsianSub1618T=0.760C=0.240
The Genome Aggregation DatabaseEuropeSub18498T=0.943C=0.056
The Genome Aggregation DatabaseGlobalStudy-wide29972T=0.791C=0.208
The Genome Aggregation DatabaseOtherSub302T=0.860C=0.140
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.715C=0.284
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.933C=0.067
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
rs8385300.000925alcohol dependence20201924

eQTL of rs838530 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 rs838530 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 )
chr1119868870119869562E070-27937
chr1119872303119872476E070-25023
chr1119872525119872715E070-24784
chr1119873739119873850E070-23649
chr1119873922119873989E070-23510
chr1119890560119890680E070-6819
chr1119890743119890831E070-6668
chr1119891029119891079E070-6420
chr1119872303119872476E071-25023
chr1119903829119904359E0746330
chr1119904383119904433E0746884



Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr1119869604119870819E067-26680
chr1119869604119870819E068-26680
chr1119869604119870819E069-26680
chr1119869604119870819E070-26680
chr1119869604119870819E071-26680
chr1119869604119870819E072-26680
chr1119869604119870819E073-26680
chr1119869604119870819E074-26680
chr1119869604119870819E082-26680