rs12889050

Homo sapiens
C>T
LOC644919 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0090 (2716/29942,GnomAD)
T=0072 (2103/29118,TOPMED)
T=0041 (204/5008,1000G)
T=0125 (480/3854,ALSPAC)
T=0127 (470/3708,TWINSUK)
chr14:40971126 (GRCh38.p7) (14q21.1)
AD
GWASdb2
1   publication(s)
See rs on genome
3 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 14NC_000014.9:g.40971126C>T
GRCh37.p13 chr 14NC_000014.8:g.41440331C>T

Gene: LOC644919, uncharacterized LOC644919(plus strand)

Molecule type Change Amino acid[Codon] SO Term
LINC02315 transcript variant 1NR_109757.1:n.N/AIntron Variant
LINC02315 transcript variant 2NR_109758.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.996T=0.004
1000GenomesAmericanSub694C=0.950T=0.050
1000GenomesEast AsianSub1008C=0.999T=0.001
1000GenomesEuropeSub1006C=0.861T=0.139
1000GenomesGlobalStudy-wide5008C=0.959T=0.041
1000GenomesSouth AsianSub978C=0.970T=0.030
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.875T=0.125
The Genome Aggregation DatabaseAfricanSub8730C=0.977T=0.023
The Genome Aggregation DatabaseAmericanSub836C=0.930T=0.070
The Genome Aggregation DatabaseEast AsianSub1610C=0.999T=0.001
The Genome Aggregation DatabaseEuropeSub18466C=0.867T=0.132
The Genome Aggregation DatabaseGlobalStudy-wide29942C=0.909T=0.090
The Genome Aggregation DatabaseOtherSub300C=0.930T=0.070
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.927T=0.072
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.873T=0.127
PMID Title Author Journal
21956439Genome-wide association study of alcohol dependence implicates KIAA0040 on chromosome 1q.Zuo LNeuropsychopharmacology

P-Value

SNP ID p-value Traits Study
rs128890507E-06alcohol dependence21956439

eQTL of rs12889050 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 rs12889050 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 )
chr144143725941437309E074-3022
chr144143762941437679E074-2652
chr144143776441437819E074-2512