rs1970008

Homo sapiens
A>G
CASC20 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A==0289 (8652/29892,GnomAD)
A==0296 (8633/29118,TOPMED)
A==0238 (1193/5008,1000G)
A==0269 (1036/3854,ALSPAC)
A==0275 (1020/3708,TWINSUK)
chr20:6487724 (GRCh38.p7) (20p12.3)
AD
GWASdb2
2   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.6487724A>G
GRCh37.p13 chr 20NC_000020.10:g.6468371A>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
1000GenomesAfricanSub1322A=0.342G=0.658
1000GenomesAmericanSub694A=0.230G=0.770
1000GenomesEast AsianSub1008A=0.114G=0.886
1000GenomesEuropeSub1006A=0.261G=0.739
1000GenomesGlobalStudy-wide5008A=0.238G=0.762
1000GenomesSouth AsianSub978A=0.210G=0.790
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.269G=0.731
The Genome Aggregation DatabaseAfricanSub8710A=0.341G=0.659
The Genome Aggregation DatabaseAmericanSub834A=0.280G=0.720
The Genome Aggregation DatabaseEast AsianSub1612A=0.125G=0.875
The Genome Aggregation DatabaseEuropeSub18434A=0.280G=0.719
The Genome Aggregation DatabaseGlobalStudy-wide29892A=0.289G=0.710
The Genome Aggregation DatabaseOtherSub302A=0.260G=0.740
Trans-Omics for Precision MedicineGlobalStudy-wide29118A=0.296G=0.703
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.275G=0.725
PMID Title Author Journal
20201924Genome-wide association study of alcohol dependence implicates a region on chromosome 11.Edenberg HJAlcohol Clin Exp Res
17186469Mutations in the gene encoding the Wnt-signaling component R-spondin 4 (RSPO4) cause autosomal recessive anonychia.Bergmann CAm J Hum Genet

P-Value

SNP ID p-value Traits Study
rs19700080.00083alcohol dependence20201924

eQTL of rs1970008 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 rs1970008 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 )
chr2064699836471086E0701612
chr2064727216472798E0714350
chr2064722646472381E0723893
chr2064725016472551E0724130



Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr2064728216473703E0674450
chr2065140046515204E06745633
chr2064728216473703E0684450
chr2065140046515204E06845633
chr2064728216473703E0694450
chr2065140046515204E06945633
chr2065140046515204E07045633
chr2064728216473703E0714450
chr2065140046515204E07145633
chr2064728216473703E0724450
chr2065140046515204E07245633
chr2064728216473703E0734450
chr2065140046515204E07345633
chr2064728216473703E0744450
chr2065140046515204E07445633
chr2065140046515204E08145633
chr2065140046515204E08245633