rs1593000

Homo sapiens
C>T
ZNF563 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0225 (6733/29846,GnomAD)
T=0245 (7138/29118,TOPMED)
T=0223 (1117/5008,1000G)
T=0171 (659/3854,ALSPAC)
T=0160 (593/3708,TWINSUK)
chr19:12329054 (GRCh38.p7) (19p13.2)
AD
GWASdb2
1   publication(s)
See rs on genome
15 Enhancers around
29 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 19NC_000019.10:g.12329054C>T
GRCh37.p13 chr 19NC_000019.9:g.12439868C>T

Gene: ZNF563, zinc finger protein 563(minus strand)

Molecule type Change Amino acid[Codon] SO Term
ZNF563 transcript variant 1NM_145276.2:c.N/AIntron Variant
ZNF563 transcript variant X6XM_005259750.4:c.N/AIntron Variant
ZNF563 transcript variant X7XM_005259751.3:c.N/AIntron Variant
ZNF563 transcript variant X2XM_006722650.3:c.N/AIntron Variant
ZNF563 transcript variant X5XM_006722651.3:c.N/AIntron Variant
ZNF563 transcript variant X3XM_011527700.2:c.N/AIntron Variant
ZNF563 transcript variant X1XM_011527698.1:c.N/AGenic Upstream Transcript Variant
ZNF563 transcript variant X4XM_011527699.2:c.N/AGenic Upstream Transcript Variant
ZNF563 transcript variant X7XM_017026332.1:c.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.660T=0.340
1000GenomesAmericanSub694C=0.830T=0.170
1000GenomesEast AsianSub1008C=0.766T=0.234
1000GenomesEuropeSub1006C=0.830T=0.170
1000GenomesGlobalStudy-wide5008C=0.777T=0.223
1000GenomesSouth AsianSub978C=0.860T=0.140
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.829T=0.171
The Genome Aggregation DatabaseAfricanSub8700C=0.680T=0.320
The Genome Aggregation DatabaseAmericanSub834C=0.850T=0.150
The Genome Aggregation DatabaseEast AsianSub1616C=0.721T=0.279
The Genome Aggregation DatabaseEuropeSub18394C=0.818T=0.181
The Genome Aggregation DatabaseGlobalStudy-wide29846C=0.774T=0.225
The Genome Aggregation DatabaseOtherSub302C=0.870T=0.130
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.754T=0.245
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.840T=0.160
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
rs15930000.000231alcohol dependence20201924

eQTL of rs1593000 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr19:12439868PRKCSHENSG00000130175.5C>T6.3818e-8893759Cerebellum

meQTL of rs1593000 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 )
chr191247460812474657E06734740
chr191244515312445216E0685285
chr191240347112403514E070-36354
chr191240355012403635E070-36233
chr191244515312445216E0705285
chr191244515312445216E0715285
chr191244515312445216E0725285
chr191240335312403426E073-36442
chr191240347112403514E073-36354
chr191240355012403635E073-36233
chr191247419112474310E07334323
chr191239002212390072E074-49796
chr191247419112474310E07434323
chr191240347112403514E082-36354
chr191240355012403635E082-36233








Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr191240434612406467E067-33401
chr191244335312445037E0673485
chr191247528812477355E06735420
chr191240434612406467E068-33401
chr191244335312445037E0683485
chr191247528812477355E06835420
chr191240434612406467E069-33401
chr191244335312445037E0693485
chr191247528812477355E06935420
chr191240434612406467E070-33401
chr191244335312445037E0703485
chr191247528812477355E07035420
chr191240434612406467E071-33401
chr191244335312445037E0713485
chr191247528812477355E07135420
chr191240434612406467E072-33401
chr191244335312445037E0723485
chr191247528812477355E07235420
chr191240434612406467E073-33401
chr191244335312445037E0733485
chr191247528812477355E07335420
chr191240434612406467E074-33401
chr191244335312445037E0743485
chr191247528812477355E07435420
chr191240434612406467E081-33401
chr191244335312445037E0813485
chr191240434612406467E082-33401
chr191244335312445037E0823485
chr191247528812477355E08235420