rs13295927

Homo sapiens
T>C
SHC3 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0106 (3200/29924,GnomAD)
C=0093 (2714/29118,TOPMED)
C=0061 (307/5008,1000G)
C=0178 (686/3854,ALSPAC)
C=0174 (646/3708,TWINSUK)
chr9:89117794 (GRCh38.p7) (9q22.1)
AD
GWASdb2
1   publication(s)
See rs on genome
26 Enhancers around
4 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 9NC_000009.12:g.89117794T>C
GRCh37.p13 chr 9NC_000009.11:g.91732709T>C

Gene: SHC3, SHC (Src homology 2 domain containing) transforming protein 3(minus strand)

Molecule type Change Amino acid[Codon] SO Term
SHC3 transcriptNM_016848.5:c.N/AIntron Variant
SHC3 transcript variant X1XM_011518785.2:c.N/AIntron Variant
SHC3 transcript variant X3XM_017014809.1:c.N/AIntron Variant
SHC3 transcript variant X4XM_017014810.1:c.N/AIntron Variant
SHC3 transcript variant X2XM_011518786.2:c.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.997C=0.003
1000GenomesAmericanSub694T=0.920C=0.080
1000GenomesEast AsianSub1008T=0.988C=0.012
1000GenomesEuropeSub1006T=0.848C=0.152
1000GenomesGlobalStudy-wide5008T=0.939C=0.061
1000GenomesSouth AsianSub978T=0.920C=0.080
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.822C=0.178
The Genome Aggregation DatabaseAfricanSub8730T=0.971C=0.029
The Genome Aggregation DatabaseAmericanSub838T=0.940C=0.060
The Genome Aggregation DatabaseEast AsianSub1612T=0.989C=0.011
The Genome Aggregation DatabaseEuropeSub18442T=0.845C=0.154
The Genome Aggregation DatabaseGlobalStudy-wide29924T=0.893C=0.106
The Genome Aggregation DatabaseOtherSub302T=0.900C=0.100
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.906C=0.093
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.826C=0.174
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
rs132959270.0000063alcohol dependence20201924
rs132959270.00000631alcoholismpha002893
rs132959270.00043alcohol dependence(early age of onset)20201924

eQTL of rs13295927 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 rs13295927 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 )
chr99169279591693049E067-39660
chr99169318291693282E067-39427
chr99169336891693431E067-39278
chr99169353791693729E067-38980
chr99169427891695531E067-37178
chr99175258691753179E06719877
chr99169427891695531E068-37178
chr99176923691770012E06836527
chr99177004691770096E06837337
chr99169427891695531E069-37178
chr99176823491769019E06935525
chr99169427891695531E071-37178
chr99175258691753179E07219877
chr99176823491769019E07235525
chr99169279591693049E073-39660
chr99169318291693282E073-39427
chr99169336891693431E073-39278
chr99169353791693729E073-38980
chr99169427891695531E073-37178
chr99175258691753179E07319877
chr99172674891726843E081-5866
chr99172695791727144E081-5565
chr99172720391727354E081-5355
chr99172746991727537E081-5172
chr99177580491775863E08243095
chr99177589191776003E08243182








Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr99176009291760358E06927383
chr99176009291760358E07127383
chr99176009291760358E07227383
chr99176009291760358E07327383