rs2017246

Homo sapiens
A>G
JPH2 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A==0402 (11976/29752,GnomAD)
A==0416 (12122/29118,TOPMED)
A==0414 (2075/5008,1000G)
A==0410 (1581/3854,ALSPAC)
A==0405 (1500/3708,TWINSUK)
chr20:44147203 (GRCh38.p7) (20q13.12)
AD
GWASdb2
1   publication(s)
See rs on genome
1 Enhancer around
2 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 20NC_000020.11:g.44147203A>G
GRCh37.p13 chr 20NC_000020.10:g.42775843A>G
JPH2 RefSeqGene LRG_394

Gene: JPH2, junctophilin 2(minus strand)

Molecule type Change Amino acid[Codon] SO Term
JPH2 transcript variant 1NM_020433.4:c.N/AIntron Variant
JPH2 transcript variant 2NM_175913.3:c.N/AGenic Downstream Transcript Variant
JPH2 transcript variant X1XM_006723833.3:c.N/AGenic Downstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322A=0.448G=0.552
1000GenomesAmericanSub694A=0.430G=0.570
1000GenomesEast AsianSub1008A=0.425G=0.575
1000GenomesEuropeSub1006A=0.414G=0.586
1000GenomesGlobalStudy-wide5008A=0.414G=0.586
1000GenomesSouth AsianSub978A=0.350G=0.650
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.410G=0.590
The Genome Aggregation DatabaseAfricanSub8652A=0.406G=0.594
The Genome Aggregation DatabaseAmericanSub834A=0.490G=0.510
The Genome Aggregation DatabaseEast AsianSub1596A=0.449G=0.551
The Genome Aggregation DatabaseEuropeSub18368A=0.392G=0.607
The Genome Aggregation DatabaseGlobalStudy-wide29752A=0.402G=0.597
The Genome Aggregation DatabaseOtherSub302A=0.420G=0.580
Trans-Omics for Precision MedicineGlobalStudy-wide29118A=0.416G=0.583
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.405G=0.595
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
rs20172460.000627alcohol dependence20201924

eQTL of rs2017246 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 rs2017246 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 )
chr204281009642810598E06934253

Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr204281481142817304E06938968
chr204281481142817304E07438968