rs28507852

Homo sapiens
T>A
CDH13 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0439 (13161/29916,GnomAD)
A=0413 (12028/29118,TOPMED)
A=0396 (1985/5008,1000G)
T==0477 (1837/3854,ALSPAC)
T==0462 (1713/3708,TWINSUK)
chr16:83121720 (GRCh38.p7) (16q23.3)
AD
GWASdb2
1   publication(s)
See rs on genome
40 Enhancers around
9 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 16NC_000016.10:g.83121720T>A
GRCh37.p13 chr 16NC_000016.9:g.83155325T>A

Gene: CDH13, cadherin 13(plus strand)

Molecule type Change Amino acid[Codon] SO Term
CDH13 transcript variant 2NM_001220488.1:c.N/AIntron Variant
CDH13 transcript variant 3NM_001220489.1:c.N/AIntron Variant
CDH13 transcript variant 4NM_001220490.1:c.N/AIntron Variant
CDH13 transcript variant 5NM_001220491.1:c.N/AIntron Variant
CDH13 transcript variant 6NM_001220492.1:c.N/AIntron Variant
CDH13 transcript variant 1NM_001257.4:c.N/AIntron Variant
CDH13 transcript variant X1XM_011522804.2:c.N/AIntron Variant
CDH13 transcript variant X2XM_017022848.1:c.N/AIntron Variant
CDH13 transcript variant X3XM_017022849.1:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.747A=0.253
1000GenomesAmericanSub694T=0.440A=0.560
1000GenomesEast AsianSub1008T=0.699A=0.301
1000GenomesEuropeSub1006T=0.470A=0.530
1000GenomesGlobalStudy-wide5008T=0.604A=0.396
1000GenomesSouth AsianSub978T=0.570A=0.430
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.477A=0.523
The Genome Aggregation DatabaseAfricanSub8714T=0.724A=0.276
The Genome Aggregation DatabaseAmericanSub834T=0.370A=0.630
The Genome Aggregation DatabaseEast AsianSub1614T=0.667A=0.333
The Genome Aggregation DatabaseEuropeSub18456T=0.480A=0.519
The Genome Aggregation DatabaseGlobalStudy-wide29916T=0.560A=0.439
The Genome Aggregation DatabaseOtherSub298T=0.650A=0.350
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.586A=0.413
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.462A=0.538
PMID Title Author Journal
23743675A meta-analysis of two genome-wide association studies to identify novel loci for maximum number of alcoholic drinks.Kapoor MHum Genet

P-Value

SNP ID p-value Traits Study
rs285078525.05E-05alcohol consumption23743675

eQTL of rs28507852 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 rs28507852 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 )
chr168314751483147727E068-7598
chr168317232583172440E06817000
chr168317258583172635E06817260
chr168317966583179715E06824340
chr168317993483179978E06824609
chr168318010383180174E06824778
chr168314702283147275E069-8050
chr168314751483147727E069-7598
chr168314840983148685E069-6640
chr168316846083168510E06913135
chr168317045983170699E06915134
chr168317733083177916E06922005
chr168314702283147275E071-8050
chr168316869683168785E07113371
chr168317045983170699E07115134
chr168317733083177916E07122005
chr168317966583179715E07124340
chr168317993483179978E07124609
chr168318010383180174E07124778
chr168314702283147275E072-8050
chr168314751483147727E072-7598
chr168317045983170699E07215134
chr168317232583172440E07217000
chr168317966583179715E07224340
chr168317993483179978E07224609
chr168318010383180174E07224778
chr168314702283147275E074-8050
chr168316846083168510E07413135
chr168316869683168785E07413371
chr168317733083177916E07422005
chr168317993483179978E07424609
chr168318010383180174E07424778
chr168310827183108371E081-46954
chr168310864283108692E081-46633
chr168310906583109305E081-46020
chr168310934483110439E081-44886
chr168311665583116748E081-38577
chr168311681683117356E081-37969
chr168310906583109305E082-46020
chr168311665583116748E082-38577







Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr168317073483171415E06715409
chr168317073483171415E06815409
chr168317073483171415E06915409
chr168317073483171415E07115409
chr168317144983171780E07116124
chr168317073483171415E07215409
chr168317144983171780E07216124
chr168317073483171415E07415409
chr168317144983171780E07416124