rs1501558

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

KCNH1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

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)

Position: chr1:210953065 (GRCh38.p7) (1q32.2)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 66 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.210953065G>A
GRCh37.p13 chr 1	NC_000001.10:g.211126407G>A
KCNH1 RefSeqGene	NG_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 2	NM_002238.3:c.	N/A	Intron Variant
KCNH1 transcript variant 1	NM_172362.2:c.	N/A	Intron Variant
KCNH1 transcript variant X1	XM_017001246.1:c.	N/A	Genic Upstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.677	A=0.323
1000Genomes	American	Sub	694	G=0.700	A=0.300
1000Genomes	East Asian	Sub	1008	G=0.914	A=0.086
1000Genomes	Europe	Sub	1006	G=0.645	A=0.355
1000Genomes	Global	Study-wide	5008	G=0.730	A=0.270
1000Genomes	South Asian	Sub	978	G=0.720	A=0.280
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.626	A=0.374
The Genome Aggregation Database	African	Sub	8704	G=0.673	A=0.327
The Genome Aggregation Database	American	Sub	838	G=0.750	A=0.250
The Genome Aggregation Database	East Asian	Sub	1620	G=0.926	A=0.074
The Genome Aggregation Database	Europe	Sub	18462	G=0.601	A=0.398
The Genome Aggregation Database	Global	Study-wide	29926	G=0.644	A=0.355
The Genome Aggregation Database	Other	Sub	302	G=0.640	A=0.360
Trans-Omics for Precision Medicine	Global	Study-wide	29116	G=0.664	A=0.335
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.625	A=0.375

PMID	Title	Author	Journal
20201924	Genome-wide association study of alcohol dependence implicates a region on chromosome 11.	Edenberg HJ	Alcohol Clin Exp Res

P-Value

SNP ID	p-value	Traits	Study
rs1501558	0.000306	alcohol dependence	20201924

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 )
chr1	211078097	211078153	E067	-48254
chr1	211079289	211079866	E067	-46541
chr1	211080737	211080860	E067	-45547
chr1	211080906	211080976	E067	-45431
chr1	211081471	211081829	E067	-44578
chr1	211081886	211081979	E067	-44428
chr1	211082065	211082515	E067	-43892
chr1	211082619	211082833	E067	-43574
chr1	211090929	211091826	E067	-34581
chr1	211079289	211079866	E068	-46541
chr1	211080202	211080282	E068	-46125
chr1	211080737	211080860	E068	-45547
chr1	211080906	211080976	E068	-45431
chr1	211081471	211081829	E068	-44578
chr1	211081886	211081979	E068	-44428
chr1	211082065	211082515	E068	-43892
chr1	211082619	211082833	E068	-43574
chr1	211090929	211091826	E068	-34581
chr1	211096843	211096988	E068	-29419
chr1	211078097	211078153	E069	-48254
chr1	211079289	211079866	E069	-46541
chr1	211081471	211081829	E069	-44578
chr1	211081886	211081979	E069	-44428
chr1	211082065	211082515	E069	-43892
chr1	211082619	211082833	E069	-43574
chr1	211085507	211085557	E069	-40850
chr1	211090929	211091826	E069	-34581
chr1	211078097	211078153	E071	-48254
chr1	211079289	211079866	E071	-46541
chr1	211080202	211080282	E071	-46125
chr1	211080737	211080860	E071	-45547
chr1	211080906	211080976	E071	-45431
chr1	211081471	211081829	E071	-44578
chr1	211081886	211081979	E071	-44428
chr1	211082065	211082515	E071	-43892
chr1	211082619	211082833	E071	-43574
chr1	211090929	211091826	E071	-34581
chr1	211078097	211078153	E072	-48254
chr1	211079289	211079866	E072	-46541
chr1	211080202	211080282	E072	-46125
chr1	211080906	211080976	E072	-45431
chr1	211081471	211081829	E072	-44578
chr1	211081886	211081979	E072	-44428
chr1	211082065	211082515	E072	-43892
chr1	211082619	211082833	E072	-43574
chr1	211083327	211083632	E072	-42775
chr1	211083688	211083895	E072	-42512
chr1	211085507	211085557	E072	-40850
chr1	211090929	211091826	E072	-34581
chr1	211080737	211080860	E073	-45547
chr1	211080906	211080976	E073	-45431
chr1	211081471	211081829	E073	-44578
chr1	211081886	211081979	E073	-44428
chr1	211082065	211082515	E073	-43892
chr1	211082619	211082833	E073	-43574
chr1	211090929	211091826	E073	-34581
chr1	211079289	211079866	E074	-46541
chr1	211080202	211080282	E074	-46125
chr1	211080737	211080860	E074	-45547
chr1	211080906	211080976	E074	-45431
chr1	211081471	211081829	E074	-44578
chr1	211081886	211081979	E074	-44428
chr1	211082065	211082515	E074	-43892
chr1	211082619	211082833	E074	-43574
chr1	211090929	211091826	E074	-34581
chr1	211124672	211124964	E081	-1443