rs3731539

Homo sapiens
C>T
CDC25A : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C==0005 (635/109766,ExAC)
C==0020 (610/29956,GnomAD)
C==0030 (875/29118,TOPMED)
T=0021 (154/7272,GO-ESP)
C==0026 (128/5008,1000G)
C==0000 (0/3854,ALSPAC)
C==0000 (0/3708,TWINSUK)
chr3:48167996 (GRCh38.p7) (3p21.31)
AD
GWASdb2
1   publication(s)
See rs on genome
55 Enhancers around
9 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 3NC_000003.12:g.48167996C>T
GRCh37.p13 chr 3NC_000003.11:g.48209486C>T

Gene: CDC25A, cell division cycle 25A(minus strand)

Molecule type Change Amino acid[Codon] SO Term
CDC25A transcript variant 1NM_001789.2:c.N/AIntron Variant
CDC25A transcript variant 2NM_201567.1:c.N/AIntron Variant
CDC25A transcript variant X2XM_006713434.2:c.N/AIntron Variant
CDC25A transcript variant X3XM_006713435.2:c.N/AIntron Variant
CDC25A transcript variant X1XM_011534316.1:c.N/AIntron Variant
CDC25A transcript variant X4XR_001740392.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.092T=0.908
1000GenomesAmericanSub694C=0.010T=0.990
1000GenomesEast AsianSub1008C=0.000T=1.000
1000GenomesEuropeSub1006C=0.001T=0.999
1000GenomesGlobalStudy-wide5008C=0.026T=0.974
1000GenomesSouth AsianSub978C=0.000T=1.000
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.000T=1.000
The Exome Aggregation ConsortiumAmericanSub19770C=0.031T=0.968
The Exome Aggregation ConsortiumAsianSub23306C=0.000T=1.000
The Exome Aggregation ConsortiumEuropeSub65850C=0.000T=0.999
The Exome Aggregation ConsortiumGlobalStudy-wide109766C=0.005T=0.994
The Exome Aggregation ConsortiumOtherSub840C=0.000T=1.000
The Genome Aggregation DatabaseAfricanSub8718C=0.070T=0.930
The Genome Aggregation DatabaseAmericanSub838C=0.000T=1.000
The Genome Aggregation DatabaseEast AsianSub1616C=0.000T=1.000
The Genome Aggregation DatabaseEuropeSub18482C=0.000T=1.000
The Genome Aggregation DatabaseGlobalStudy-wide29956C=0.020T=0.979
The Genome Aggregation DatabaseOtherSub302C=0.000T=1.000
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.030T=0.969
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.000T=1.000
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
rs37315390.000612alcohol dependence20201924

eQTL of rs3731539 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 rs3731539 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 )
chr34817130748171437E067-38049
chr34817144748172697E067-36789
chr34817278948172839E067-36647
chr34817288348173012E067-36474
chr34817730848177701E067-31785
chr34819253748194056E067-15430
chr34817130748171437E068-38049
chr34817144748172697E068-36789
chr34817278948172839E068-36647
chr34817288348173012E068-36474
chr34817730848177701E068-31785
chr34817774648177873E068-31613
chr34823566448236546E06826178
chr34825654448256814E06847058
chr34825682048257796E06847334
chr34817130748171437E069-38049
chr34817144748172697E069-36789
chr34817278948172839E069-36647
chr34817730848177701E069-31785
chr34819253748194056E069-15430
chr34825824348258295E06948757
chr34817144748172697E070-36789
chr34817278948172839E070-36647
chr34817288348173012E070-36474
chr34822744848227558E07017962
chr34825682048257796E07047334
chr34817130748171437E071-38049
chr34817288348173012E071-36474
chr34817730848177701E071-31785
chr34817774648177873E071-31613
chr34823566448236546E07126178
chr34825682048257796E07147334
chr34817130748171437E072-38049
chr34817144748172697E072-36789
chr34817278948172839E072-36647
chr34817288348173012E072-36474
chr34817730848177701E072-31785
chr34819253748194056E072-15430
chr34825654448256814E07247058
chr34825682048257796E07247334
chr34825824348258295E07248757
chr34817130748171437E073-38049
chr34817144748172697E073-36789
chr34817278948172839E073-36647
chr34817288348173012E073-36474
chr34817730848177701E073-31785
chr34819253748194056E073-15430
chr34817130748171437E074-38049
chr34817144748172697E074-36789
chr34817730848177701E074-31785
chr34817774648177873E074-31613
chr34823566448236546E07426178
chr34825654448256814E07447058
chr34825908048259152E07449594
chr34822811648228190E08218630









Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr34822854048230649E06719054
chr34822854048230649E06819054
chr34822854048230649E06919054
chr34822854048230649E07019054
chr34822854048230649E07119054
chr34822854048230649E07219054
chr34822854048230649E07319054
chr34822854048230649E07419054
chr34822854048230649E08219054