rs9593517

Homo sapiens
A>G
LINC00377 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
G=0329 (9847/29898,GnomAD)
G=0370 (10790/29118,TOPMED)
G=0421 (2106/5008,1000G)
G=0263 (1015/3854,ALSPAC)
G=0254 (941/3708,TWINSUK)
chr13:81019942 (GRCh38.p7) (13q31.1)
AD
GWASdb2
1   publication(s)
See rs on genome
10 Enhancers around
27 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 13NC_000013.11:g.81019942A>G
GRCh37.p13 chr 13NC_000013.10:g.81594077A>G

Gene: LINC00377, long intergenic non-protein coding RNA 377(plus strand)

Molecule type Change Amino acid[Codon] SO Term
LINC00377 transcriptNR_125770.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322A=0.399G=0.601
1000GenomesAmericanSub694A=0.730G=0.270
1000GenomesEast AsianSub1008A=0.655G=0.345
1000GenomesEuropeSub1006A=0.769G=0.231
1000GenomesGlobalStudy-wide5008A=0.579G=0.421
1000GenomesSouth AsianSub978A=0.440G=0.560
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.737G=0.263
The Genome Aggregation DatabaseAfricanSub8702A=0.473G=0.527
The Genome Aggregation DatabaseAmericanSub832A=0.690G=0.310
The Genome Aggregation DatabaseEast AsianSub1614A=0.667G=0.333
The Genome Aggregation DatabaseEuropeSub18448A=0.759G=0.240
The Genome Aggregation DatabaseGlobalStudy-wide29898A=0.670G=0.329
The Genome Aggregation DatabaseOtherSub302A=0.880G=0.120
Trans-Omics for Precision MedicineGlobalStudy-wide29118A=0.629G=0.370
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.746G=0.254
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
rs95935170.000989alcohol dependence20201924

eQTL of rs9593517 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr13:81594077RP11-521J24.1ENSG00000229246.1A>G6.7889e-9-23728Cerebellum

meQTL of rs9593517 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 )
chr138159049181591077E067-3000
chr138159123781591287E067-2790
chr138163572181636292E06741644
chr138156385681564200E069-29877
chr138159049181591077E069-3000
chr138159123781591287E069-2790
chr138163572181636292E06941644
chr138159049181591077E072-3000
chr138159123781591287E072-2790
chr138156385681564200E074-29877




Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr138156284781562905E067-31172
chr138156294681563247E067-30830
chr138162232481622614E06728247
chr138156284781562905E068-31172
chr138156294681563247E068-30830
chr138156334581563405E068-30672
chr138159143581592190E068-1887
chr138162232481622614E06828247
chr138156284781562905E069-31172
chr138156294681563247E069-30830
chr138156334581563405E069-30672
chr138159143581592190E069-1887
chr138162232481622614E06928247
chr138156294681563247E071-30830
chr138156334581563405E071-30672
chr138159143581592190E071-1887
chr138162232481622614E07128247
chr138156284781562905E072-31172
chr138156294681563247E072-30830
chr138156334581563405E072-30672
chr138159143581592190E072-1887
chr138162232481622614E07228247
chr138159143581592190E073-1887
chr138156284781562905E074-31172
chr138156294681563247E074-30830
chr138156334581563405E074-30672
chr138162232481622614E07428247