rs11586125

Homo sapiens
T>C
LOC107984931 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0293 (8763/29912,GnomAD)
C=0317 (9258/29118,TOPMED)
C=0409 (2047/5008,1000G)
C=0210 (810/3854,ALSPAC)
C=0197 (731/3708,TWINSUK)
chr1:24050836 (GRCh38.p7) (1p36.11)
AD
GWASdb2
1   publication(s)
See rs on genome
18 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 1NC_000001.11:g.24050836T>C
GRCh37.p13 chr 1NC_000001.10:g.24377326T>C

Gene: LOC107984931, uncharacterized LOC107984931(plus strand)

Molecule type Change Amino acid[Codon] SO Term
LOC107984931 transcriptXR_001737929.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.551C=0.449
1000GenomesAmericanSub694T=0.790C=0.210
1000GenomesEast AsianSub1008T=0.415C=0.585
1000GenomesEuropeSub1006T=0.770C=0.230
1000GenomesGlobalStudy-wide5008T=0.591C=0.409
1000GenomesSouth AsianSub978T=0.510C=0.490
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.790C=0.210
The Genome Aggregation DatabaseAfricanSub8710T=0.585C=0.415
The Genome Aggregation DatabaseAmericanSub836T=0.730C=0.270
The Genome Aggregation DatabaseEast AsianSub1610T=0.406C=0.594
The Genome Aggregation DatabaseEuropeSub18454T=0.790C=0.209
The Genome Aggregation DatabaseGlobalStudy-wide29912T=0.707C=0.293
The Genome Aggregation DatabaseOtherSub302T=0.690C=0.310
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.682C=0.317
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.803C=0.197
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
rs115861250.00042alcohol dependence(early age of onset)20201924
rs115861250.00079alcohol dependence20201924

eQTL of rs11586125 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr1:24377326PNRC2ENSG00000189266.7T>C1.5432e-2091727Cerebellum
Chr1:24377326PNRC2ENSG00000189266.7T>C1.0478e-2491727Cortex
Chr1:24377326PNRC2ENSG00000189266.7T>C2.6746e-2191727Anterior_cingulate_cortex

meQTL of rs11586125 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 )
chr12434502424345901E069-31425
chr12434601524346116E069-31210
chr12434502424345901E070-31425
chr12437267624373198E070-4128
chr12437324124373337E070-3989
chr12439728824397819E07019962
chr12434502424345901E071-31425
chr12439728824397819E07219962
chr12434502424345901E073-31425
chr12434419724344247E081-33079
chr12434428924344347E081-32979
chr12434467124344744E081-32582
chr12434502424345901E081-31425
chr12434601524346116E081-31210
chr12434502424345901E082-31425
chr12437230924372611E082-4715
chr12437267624373198E082-4128
chr12439728824397819E08219962