rs1501558

Homo sapiens
G>A
KCNH1 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0355 (10645/29926,GnomAD)
A=0335 (9766/29116,TOPMED)
A=0270 (1353/5008,1000G)
A=0374 (1441/3854,ALSPAC)
A=0375 (1390/3708,TWINSUK)
chr1:210953065 (GRCh38.p7) (1q32.2)
AD
GWASdb2
1   publication(s)
See rs on genome
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 1NC_000001.11:g.210953065G>A
GRCh37.p13 chr 1NC_000001.10:g.211126407G>A
KCNH1 RefSeqGeneNG_029777.1:g.186051C>T

Gene: KCNH1, potassium voltage-gated channel subfamily H member 1(minus strand)

Molecule type Change Amino acid[Codon] SO Term
KCNH1 transcript variant 2NM_002238.3:c.N/AIntron Variant
KCNH1 transcript variant 1NM_172362.2:c.N/AIntron Variant
KCNH1 transcript variant X1XM_017001246.1:c.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.677A=0.323
1000GenomesAmericanSub694G=0.700A=0.300
1000GenomesEast AsianSub1008G=0.914A=0.086
1000GenomesEuropeSub1006G=0.645A=0.355
1000GenomesGlobalStudy-wide5008G=0.730A=0.270
1000GenomesSouth AsianSub978G=0.720A=0.280
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.626A=0.374
The Genome Aggregation DatabaseAfricanSub8704G=0.673A=0.327
The Genome Aggregation DatabaseAmericanSub838G=0.750A=0.250
The Genome Aggregation DatabaseEast AsianSub1620G=0.926A=0.074
The Genome Aggregation DatabaseEuropeSub18462G=0.601A=0.398
The Genome Aggregation DatabaseGlobalStudy-wide29926G=0.644A=0.355
The Genome Aggregation DatabaseOtherSub302G=0.640A=0.360
Trans-Omics for Precision MedicineGlobalStudy-wide29116G=0.664A=0.335
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.625A=0.375
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
rs15015580.000306alcohol dependence20201924

eQTL of rs1501558 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 rs1501558 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 )
chr1211078097211078153E067-48254
chr1211079289211079866E067-46541
chr1211080737211080860E067-45547
chr1211080906211080976E067-45431
chr1211081471211081829E067-44578
chr1211081886211081979E067-44428
chr1211082065211082515E067-43892
chr1211082619211082833E067-43574
chr1211090929211091826E067-34581
chr1211079289211079866E068-46541
chr1211080202211080282E068-46125
chr1211080737211080860E068-45547
chr1211080906211080976E068-45431
chr1211081471211081829E068-44578
chr1211081886211081979E068-44428
chr1211082065211082515E068-43892
chr1211082619211082833E068-43574
chr1211090929211091826E068-34581
chr1211096843211096988E068-29419
chr1211078097211078153E069-48254
chr1211079289211079866E069-46541
chr1211081471211081829E069-44578
chr1211081886211081979E069-44428
chr1211082065211082515E069-43892
chr1211082619211082833E069-43574
chr1211085507211085557E069-40850
chr1211090929211091826E069-34581
chr1211078097211078153E071-48254
chr1211079289211079866E071-46541
chr1211080202211080282E071-46125
chr1211080737211080860E071-45547
chr1211080906211080976E071-45431
chr1211081471211081829E071-44578
chr1211081886211081979E071-44428
chr1211082065211082515E071-43892
chr1211082619211082833E071-43574
chr1211090929211091826E071-34581
chr1211078097211078153E072-48254
chr1211079289211079866E072-46541
chr1211080202211080282E072-46125
chr1211080906211080976E072-45431
chr1211081471211081829E072-44578
chr1211081886211081979E072-44428
chr1211082065211082515E072-43892
chr1211082619211082833E072-43574
chr1211083327211083632E072-42775
chr1211083688211083895E072-42512
chr1211085507211085557E072-40850
chr1211090929211091826E072-34581
chr1211080737211080860E073-45547
chr1211080906211080976E073-45431
chr1211081471211081829E073-44578
chr1211081886211081979E073-44428
chr1211082065211082515E073-43892
chr1211082619211082833E073-43574
chr1211090929211091826E073-34581
chr1211079289211079866E074-46541
chr1211080202211080282E074-46125
chr1211080737211080860E074-45547
chr1211080906211080976E074-45431
chr1211081471211081829E074-44578
chr1211081886211081979E074-44428
chr1211082065211082515E074-43892
chr1211082619211082833E074-43574
chr1211090929211091826E074-34581
chr1211124672211124964E081-1443