rs6117294

Homo sapiens
T>G
CASC20 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
G=0430 (12863/29898,GnomAD)
G=0457 (13325/29118,TOPMED)
G=0418 (2094/5008,1000G)
G=0393 (1514/3854,ALSPAC)
G=0400 (1484/3708,TWINSUK)
chr20:6490158 (GRCh38.p7) (20p12.3)
AD
GWASdb2
1   publication(s)
See rs on genome
4 Enhancers around
17 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 20NC_000020.11:g.6490158T>G
GRCh37.p13 chr 20NC_000020.10:g.6470805T>G

Gene: CASC20, cancer susceptibility candidate 20 (non-protein coding)(plus strand)

Molecule type Change Amino acid[Codon] SO Term
CASC20 transcriptNR_109953.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.441G=0.559
1000GenomesAmericanSub694T=0.650G=0.350
1000GenomesEast AsianSub1008T=0.723G=0.277
1000GenomesEuropeSub1006T=0.588G=0.412
1000GenomesGlobalStudy-wide5008T=0.582G=0.418
1000GenomesSouth AsianSub978T=0.570G=0.430
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.607G=0.393
The Genome Aggregation DatabaseAfricanSub8698T=0.459G=0.541
The Genome Aggregation DatabaseAmericanSub834T=0.640G=0.360
The Genome Aggregation DatabaseEast AsianSub1604T=0.723G=0.277
The Genome Aggregation DatabaseEuropeSub18460T=0.606G=0.393
The Genome Aggregation DatabaseGlobalStudy-wide29898T=0.569G=0.430
The Genome Aggregation DatabaseOtherSub302T=0.520G=0.480
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.542G=0.457
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.600G=0.400
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
rs61172940.0003alcohol dependence(early age of onset)20201924
rs61172940.00049alcohol dependence20201924

eQTL of rs6117294 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 rs6117294 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 )
chr2064699836471086E0700
chr2064727216472798E0711916
chr2064722646472381E0721459
chr2064725016472551E0721696



Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr2064728216473703E0672016
chr2065140046515204E06743199
chr2064728216473703E0682016
chr2065140046515204E06843199
chr2064728216473703E0692016
chr2065140046515204E06943199
chr2065140046515204E07043199
chr2064728216473703E0712016
chr2065140046515204E07143199
chr2064728216473703E0722016
chr2065140046515204E07243199
chr2064728216473703E0732016
chr2065140046515204E07343199
chr2064728216473703E0742016
chr2065140046515204E07443199
chr2065140046515204E08143199
chr2065140046515204E08243199