rs1331189

Homo sapiens
C>T
SHC3 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0060 (1809/29962,GnomAD)
T=0049 (1428/29118,TOPMED)
T=0047 (234/5008,1000G)
T=0074 (287/3854,ALSPAC)
T=0069 (257/3708,TWINSUK)
chr9:89105730 (GRCh38.p7) (9q22.1)
AD
GWASdb2
2   publication(s)
See rs on genome
24 Enhancers around
4 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 9NC_000009.12:g.89105730C>T
GRCh37.p13 chr 9NC_000009.11:g.91720645C>T

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 X2XM_011518786.2:c.N/AIntron Variant
SHC3 transcript variant X3XM_017014809.1:c.N/AIntron Variant
SHC3 transcript variant X4XM_017014810.1:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.980T=0.020
1000GenomesAmericanSub694C=0.820T=0.180
1000GenomesEast AsianSub1008C=0.998T=0.002
1000GenomesEuropeSub1006C=0.941T=0.059
1000GenomesGlobalStudy-wide5008C=0.953T=0.047
1000GenomesSouth AsianSub978C=0.980T=0.020
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.926T=0.074
The Genome Aggregation DatabaseAfricanSub8724C=0.977T=0.023
The Genome Aggregation DatabaseAmericanSub836C=0.850T=0.150
The Genome Aggregation DatabaseEast AsianSub1620C=1.000T=0.000
The Genome Aggregation DatabaseEuropeSub18480C=0.920T=0.079
The Genome Aggregation DatabaseGlobalStudy-wide29962C=0.939T=0.060
The Genome Aggregation DatabaseOtherSub302C=0.960T=0.040
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.951T=0.049
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.931T=0.069
PMID Title Author Journal
20201924Genome-wide association study of alcohol dependence implicates a region on chromosome 11.Edenberg HJAlcohol Clin Exp Res
20106866Independent and population-specific association of risk variants at the IRGM locus with Crohn's disease.Prescott NJHum Mol Genet

P-Value

SNP ID p-value Traits Study
rs13311890.00097alcohol dependence20201924

eQTL of rs1331189 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 rs1331189 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 )
chr99169279591693049E067-27596
chr99169318291693282E067-27363
chr99169336891693431E067-27214
chr99169353791693729E067-26916
chr99169427891695531E067-25114
chr99175258691753179E06731941
chr99169427891695531E068-25114
chr99176923691770012E06848591
chr99177004691770096E06849401
chr99169427891695531E069-25114
chr99176823491769019E06947589
chr99169427891695531E071-25114
chr99175258691753179E07231941
chr99176823491769019E07247589
chr99169279591693049E073-27596
chr99169318291693282E073-27363
chr99169336891693431E073-27214
chr99169353791693729E073-26916
chr99169427891695531E073-25114
chr99175258691753179E07331941
chr99172674891726843E0816103
chr99172695791727144E0816312
chr99172720391727354E0816558
chr99172746991727537E0816824







Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr99176009291760358E06939447
chr99176009291760358E07139447
chr99176009291760358E07239447
chr99176009291760358E07339447