rs673401

Homo sapiens
C>T
CDH20 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0399 (11946/29914,GnomAD)
T=0361 (10536/29118,TOPMED)
T=0306 (1533/5008,1000G)
C==0491 (1891/3854,ALSPAC)
T=0492 (1826/3708,TWINSUK)
chr18:61540199 (GRCh38.p7) (18q21.33)
AD
GWASdb2
1   publication(s)
See rs on genome
73 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 18NC_000018.10:g.61540199C>T
GRCh37.p13 chr 18NC_000018.9:g.59207432C>T

Gene: CDH20, cadherin 20(plus strand)

Molecule type Change Amino acid[Codon] SO Term
CDH20 transcriptNM_031891.3:c.N/AIntron Variant
CDH20 transcript variant X2XR_001753186.1:n.N/AIntron Variant
CDH20 transcript variant X3XR_001753187.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.848T=0.152
1000GenomesAmericanSub694C=0.660T=0.340
1000GenomesEast AsianSub1008C=0.703T=0.297
1000GenomesEuropeSub1006C=0.519T=0.481
1000GenomesGlobalStudy-wide5008C=0.694T=0.306
1000GenomesSouth AsianSub978C=0.680T=0.320
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.491T=0.509
The Genome Aggregation DatabaseAfricanSub8704C=0.781T=0.219
The Genome Aggregation DatabaseAmericanSub836C=0.690T=0.310
The Genome Aggregation DatabaseEast AsianSub1614C=0.719T=0.281
The Genome Aggregation DatabaseEuropeSub18460C=0.501T=0.498
The Genome Aggregation DatabaseGlobalStudy-wide29914C=0.600T=0.399
The Genome Aggregation DatabaseOtherSub300C=0.560T=0.440
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.638T=0.361
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.508T=0.492
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
rs6734010.000318alcohol dependence20201924

eQTL of rs673401 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 rs673401 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 )
chr185916934659170113E067-37319
chr185919796859198101E067-9331
chr185919884359198924E067-8508
chr185919900159199392E067-8040
chr185915774959157905E068-49527
chr185916271859162830E068-44602
chr185916311059163188E068-44244
chr185919788159197963E068-9469
chr185919796859198101E068-9331
chr185917133159171482E069-35950
chr185917177959171903E069-35529
chr185917415859174258E069-33174
chr185917432459174414E069-33018
chr185917464659174696E069-32736
chr185919796859198101E069-9331
chr185919855859198686E069-8746
chr185919884359198924E069-8508
chr185919796859198101E070-9331
chr185919855859198686E070-8746
chr185919884359198924E070-8508
chr185916135159161434E071-45998
chr185916148459161526E071-45906
chr185916180659161882E071-45550
chr185916217159162310E071-45122
chr185916271859162830E071-44602
chr185916311059163188E071-44244
chr185916334359163452E071-43980
chr185916357959163918E071-43514
chr185916453959164634E071-42798
chr185916934659170113E071-37319
chr185917177959171903E071-35529
chr185917432459174414E071-33018
chr185917464659174696E071-32736
chr185919788159197963E071-9469
chr185919796859198101E071-9331
chr185919855859198686E071-8746
chr185919884359198924E071-8508
chr185919900159199392E071-8040
chr185921227459212331E0714842
chr185915883559158964E072-48468
chr185916271859162830E072-44602
chr185916311059163188E072-44244
chr185916334359163452E072-43980
chr185916357959163918E072-43514
chr185917464659174696E072-32736
chr185919788159197963E072-9469
chr185919796859198101E072-9331
chr185919796859198101E073-9331
chr185919855859198686E073-8746
chr185915774959157905E074-49527
chr185916180659161882E074-45550
chr185916217159162310E074-45122
chr185916271859162830E074-44602
chr185916311059163188E074-44244
chr185916334359163452E074-43980
chr185916357959163918E074-43514
chr185916453959164634E074-42798
chr185916934659170113E074-37319
chr185917432459174414E074-33018
chr185917464659174696E074-32736
chr185919796859198101E074-9331
chr185919855859198686E074-8746
chr185919884359198924E074-8508
chr185919900159199392E074-8040
chr185921227459212331E0744842
chr185921263059212802E0745198
chr185921297359213055E0745541
chr185921307259213122E0745640
chr185919796859198101E081-9331
chr185919855859198686E081-8746
chr185923644659237070E08129014
chr185919788159197963E082-9469
chr185919796859198101E082-9331