rs2165387

Homo sapiens
T>C
LINC00989 : Intron Variant
LOC107986294 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T==0287 (8590/29912,GnomAD)
T==0293 (8539/29118,TOPMED)
T==0387 (1936/5008,1000G)
T==0261 (1004/3854,ALSPAC)
T==0239 (886/3708,TWINSUK)
chr4:79570666 (GRCh38.p7) (4q21.21)
AD
GWASdb2
1   publication(s)
See rs on genome
3 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 4NC_000004.12:g.79570666T>C
GRCh37.p13 chr 4NC_000004.11:g.80491820T>C

Gene: LINC00989, long intergenic non-protein coding RNA 989(plus strand)

Molecule type Change Amino acid[Codon] SO Term
LINC00989 transcriptNR_038826.1:n.N/AIntron Variant

Gene: LOC107986294, uncharacterized LOC107986294(plus strand)

Molecule type Change Amino acid[Codon] SO Term
LOC107986294 transcriptXR_001741747.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.362C=0.638
1000GenomesAmericanSub694T=0.240C=0.760
1000GenomesEast AsianSub1008T=0.441C=0.559
1000GenomesEuropeSub1006T=0.240C=0.760
1000GenomesGlobalStudy-wide5008T=0.387C=0.613
1000GenomesSouth AsianSub978T=0.620C=0.380
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.261C=0.739
The Genome Aggregation DatabaseAfricanSub8698T=0.347C=0.653
The Genome Aggregation DatabaseAmericanSub838T=0.260C=0.740
The Genome Aggregation DatabaseEast AsianSub1608T=0.444C=0.556
The Genome Aggregation DatabaseEuropeSub18466T=0.247C=0.752
The Genome Aggregation DatabaseGlobalStudy-wide29912T=0.287C=0.712
The Genome Aggregation DatabaseOtherSub302T=0.220C=0.780
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.293C=0.706
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.239C=0.761
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
rs21653870.000196alcohol dependence20201924

eQTL of rs2165387 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 rs2165387 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 )
chr48044786080448215E081-43605
chr48044828980448568E082-43252
chr48053089480531002E08239074