rs2589839

Homo sapiens
T>C
LINC01091 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T==0019 (573/29846,GnomAD)
T==0032 (952/29118,TOPMED)
T==0022 (112/5008,1000G)
T==0001 (5/3854,ALSPAC)
T==0001 (3/3708,TWINSUK)
chr4:123670981 (GRCh38.p7) (4q28.1)
AD
GWASdb2
1   publication(s)
See rs on genome
15 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 4NC_000004.12:g.123670981T>C
GRCh37.p13 chr 4NC_000004.11:g.124592136T>C

Gene: LINC01091, long intergenic non-protein coding RNA 1091(plus strand)

Molecule type Change Amino acid[Codon] SO Term
LINC01091 transcript variant 1NR_027105.2:n.N/AIntron Variant
LINC01091 transcript variant 2NR_027106.1:n.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.075C=0.925
1000GenomesAmericanSub694T=0.000C=1.000
1000GenomesEast AsianSub1008T=0.000C=1.000
1000GenomesEuropeSub1006T=0.002C=0.998
1000GenomesGlobalStudy-wide5008T=0.022C=0.978
1000GenomesSouth AsianSub978T=0.010C=0.990
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.001C=0.999
The Genome Aggregation DatabaseAfricanSub8710T=0.065C=0.935
The Genome Aggregation DatabaseAmericanSub828T=0.010C=0.990
The Genome Aggregation DatabaseEast AsianSub1622T=0.000C=1.000
The Genome Aggregation DatabaseEuropeSub18384T=0.000C=0.999
The Genome Aggregation DatabaseGlobalStudy-wide29846T=0.019C=0.980
The Genome Aggregation DatabaseOtherSub302T=0.000C=1.000
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.032C=0.967
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.001C=0.999
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
rs25898390.000335alcohol dependence20201924

eQTL of rs2589839 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 rs2589839 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 )
chr4124542575124542835E067-49301
chr4124542329124542453E068-49683
chr4124542575124542835E068-49301
chr4124570426124572174E068-19962
chr4124572832124572941E069-19195
chr4124542575124542835E070-49301
chr4124542329124542453E071-49683
chr4124542575124542835E071-49301
chr4124570426124572174E071-19962
chr4124542329124542453E073-49683
chr4124542575124542835E073-49301
chr4124570426124572174E081-19962
chr4124620701124622355E08128565
chr4124543908124544003E082-48133
chr4124570426124572174E082-19962