rs11856569

Homo sapiens
A>C
CASC4 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0314 (9396/29848,GnomAD)
C=0269 (7837/29118,TOPMED)
C=0290 (1452/5008,1000G)
C=0434 (1672/3854,ALSPAC)
C=0443 (1644/3708,TWINSUK)
chr15:44382642 (GRCh38.p7) (15q15.3)
AD
GWASdb2
1   publication(s)
See rs on genome
16 Enhancers around
23 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 15NC_000015.10:g.44382642A>C
GRCh37.p13 chr 15NC_000015.9:g.44674840A>C

Gene: CASC4, cancer susceptibility candidate 4(plus strand)

Molecule type Change Amino acid[Codon] SO Term
CASC4 transcript variant 1NM_138423.3:c.N/AIntron Variant
CASC4 transcript variant 2NM_177974.2:c.N/AIntron Variant
CASC4 transcript variant X2XM_017021880.1:c.N/AGenic Downstream Transcript Variant
CASC4 transcript variant X1XR_001751066.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322A=0.936C=0.064
1000GenomesAmericanSub694A=0.690C=0.310
1000GenomesEast AsianSub1008A=0.715C=0.285
1000GenomesEuropeSub1006A=0.578C=0.422
1000GenomesGlobalStudy-wide5008A=0.710C=0.290
1000GenomesSouth AsianSub978A=0.550C=0.450
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.566C=0.434
The Genome Aggregation DatabaseAfricanSub8708A=0.872C=0.128
The Genome Aggregation DatabaseAmericanSub836A=0.690C=0.310
The Genome Aggregation DatabaseEast AsianSub1606A=0.682C=0.318
The Genome Aggregation DatabaseEuropeSub18396A=0.598C=0.401
The Genome Aggregation DatabaseGlobalStudy-wide29848A=0.685C=0.314
The Genome Aggregation DatabaseOtherSub302A=0.570C=0.430
Trans-Omics for Precision MedicineGlobalStudy-wide29118A=0.730C=0.269
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.557C=0.443
PMID Title Author Journal
21703634A meta-analysis of two genome-wide association studies identifies 3 new loci for alcohol dependence.Wang KSJ Psychiatr Res

P-Value

SNP ID p-value Traits Study
rs118565691.48E-05alcohol dependence21703634

eQTL of rs11856569 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr15:44674840AC011330.5ENSG00000249839.1A>C1.7228e-14698303Cerebellum

meQTL of rs11856569 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 )
chr154467702444677196E0682184
chr154467725844677533E0682418
chr154472165944721808E06846819
chr154472212744722177E06847287
chr154472217944722267E06847339
chr154472227244722322E06847432
chr154472165944721808E06946819
chr154472165944721808E07046819
chr154472212744722177E07047287
chr154472217944722267E07047339
chr154472227244722322E07047432
chr154472165944721808E07146819
chr154472165944721808E07246819
chr154472165944721808E08146819
chr154472212744722177E08147287
chr154472217944722267E08147339






Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr154471870444720934E06743864
chr154472096444721027E06746124
chr154471809144718604E06843251
chr154471870444720934E06843864
chr154472096444721027E06846124
chr154471809144718604E06943251
chr154471870444720934E06943864
chr154471809144718604E07043251
chr154471870444720934E07043864
chr154472096444721027E07046124
chr154471870444720934E07143864
chr154472096444721027E07146124
chr154471809144718604E07243251
chr154471870444720934E07243864
chr154471870444720934E07343864
chr154472096444721027E07346124
chr154471809144718604E07443251
chr154471870444720934E07443864
chr154471870444720934E08143864
chr154472096444721027E08146124
chr154471809144718604E08243251
chr154471870444720934E08243864
chr154472096444721027E08246124