rs1889310

Homo sapiens
A>T
LINC00839 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0246 (7373/29970,GnomAD)
T=0282 (8213/29118,TOPMED)
T=0254 (1272/5008,1000G)
T=0138 (533/3854,ALSPAC)
T=0139 (515/3708,TWINSUK)
chr10:42486247 (GRCh38.p7) (10q11.21)
AD
GWASdb2
1   publication(s)
See rs on genome
0 Enhancer around
13 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 10NC_000010.11:g.42486247A>T
GRCh37.p13 chr 10NC_000010.10:g.42981695A>T

Gene: LINC00839, long intergenic non-protein coding RNA 839(plus strand)

Molecule type Change Amino acid[Codon] SO Term
LINC00839 transcriptNR_026827.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322A=0.488T=0.512
1000GenomesAmericanSub694A=0.780T=0.220
1000GenomesEast AsianSub1008A=0.964T=0.036
1000GenomesEuropeSub1006A=0.831T=0.169
1000GenomesGlobalStudy-wide5008A=0.746T=0.254
1000GenomesSouth AsianSub978A=0.760T=0.240
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.862T=0.138
The Genome Aggregation DatabaseAfricanSub8722A=0.557T=0.443
The Genome Aggregation DatabaseAmericanSub838A=0.820T=0.180
The Genome Aggregation DatabaseEast AsianSub1622A=0.949T=0.051
The Genome Aggregation DatabaseEuropeSub18486A=0.826T=0.174
The Genome Aggregation DatabaseGlobalStudy-wide29970A=0.754T=0.246
The Genome Aggregation DatabaseOtherSub302A=0.810T=0.190
Trans-Omics for Precision MedicineGlobalStudy-wide29118A=0.717T=0.282
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.861T=0.139
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
rs18893100.000846alcohol dependence20201924

eQTL of rs1889310 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr10:42981695ZNF33BENSG00000196693.10A>T2.9049e-4-108347Cortex
Chr10:42981695ZNF33BENSG00000196693.10A>T2.9552e-5-108347Putamen_basal_ganglia

meQTL of rs1889310 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.

Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr104297088242971477E067-10218
chr104297158742971719E067-9976
chr104297204842972108E067-9587
chr104297088242971477E068-10218
chr104297158742971719E068-9976
chr104297088242971477E069-10218
chr104297158742971719E069-9976
chr104297088242971477E071-10218
chr104297158742971719E071-9976
chr104297088242971477E072-10218
chr104297158742971719E072-9976
chr104297088242971477E073-10218
chr104297158742971719E073-9976