rs2640487

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

KCNA3 : Intron Variant
LOC107985174 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C==0468 (13997/29910,GnomAD)
C==0458 (13353/29118,TOPMED)
C==0499 (2499/5008,1000G)
T=0498 (1920/3854,ALSPAC)
T=0496 (1839/3708,TWINSUK)

Position: chr1:110664263 (GRCh38.p7) (1p13.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 56 Enhancers around

Promoter: 24 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.110664263C>T
GRCh37.p13 chr 1	NC_000001.10:g.111206885C>T

Gene: KCNA3, potassium voltage-gated channel subfamily A member 3(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
KCNA3 transcript variant 1	NM_002232.4:c.	N/A	Genic Downstream Transcript Variant
KCNA3 transcript variant 2	NR_109845.1:n.	N/A	Intron Variant
KCNA3 transcript variant 3	NR_109846.1:n.	N/A	Intron Variant

Gene: LOC107985174, uncharacterized LOC107985174(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC107985174 transcript variant X1	XR_001738182.1:n.	N/A	Intron Variant
LOC107985174 transcript variant X2	XR_001738183.1:n.	N/A	Intron Variant
LOC107985174 transcript variant X3	XR_001738184.1:n.	N/A	Intron Variant
LOC107985174 transcript variant X4	XR_001738185.1:n.	N/A	Intron Variant
LOC107985174 transcript variant X5	XR_001738186.1:n.	N/A	Intron Variant
LOC107985174 transcript variant X6	XR_001738187.1:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.409	T=0.591
1000Genomes	American	Sub	694	C=0.470	T=0.530
1000Genomes	East Asian	Sub	1008	C=0.517	T=0.483
1000Genomes	Europe	Sub	1006	C=0.440	T=0.560
1000Genomes	Global	Study-wide	5008	C=0.499	T=0.501
1000Genomes	South Asian	Sub	978	C=0.680	T=0.320
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.502	T=0.498
The Genome Aggregation Database	African	Sub	8716	C=0.423	T=0.577
The Genome Aggregation Database	American	Sub	838	C=0.470	T=0.530
The Genome Aggregation Database	East Asian	Sub	1606	C=0.559	T=0.441
The Genome Aggregation Database	Europe	Sub	18448	C=0.481	T=0.518
The Genome Aggregation Database	Global	Study-wide	29910	C=0.468	T=0.532
The Genome Aggregation Database	Other	Sub	302	C=0.440	T=0.560
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.458	T=0.541
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.504	T=0.496

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
rs2640487	0.00032	alcohol dependence	20201924

eQTL of rs2640487 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 rs2640487 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	111176902	111176963	E067	-29922
chr1	111177051	111177994	E067	-28891
chr1	111157562	111157602	E068	-49283
chr1	111157647	111157717	E068	-49168
chr1	111158236	111158697	E068	-48188
chr1	111176902	111176963	E068	-29922
chr1	111177051	111177994	E068	-28891
chr1	111180776	111180994	E068	-25891
chr1	111255744	111255892	E068	48859
chr1	111158236	111158697	E069	-48188
chr1	111177051	111177994	E069	-28891
chr1	111255744	111255892	E069	48859
chr1	111161664	111161792	E070	-45093
chr1	111163101	111163393	E070	-43492
chr1	111176902	111176963	E070	-29922
chr1	111177051	111177994	E070	-28891
chr1	111178132	111178259	E070	-28626
chr1	111180776	111180994	E070	-25891
chr1	111181206	111181729	E070	-25156
chr1	111186540	111186838	E070	-20047
chr1	111186923	111187075	E070	-19810
chr1	111188000	111188238	E070	-18647
chr1	111188283	111188343	E070	-18542
chr1	111188380	111188619	E070	-18266
chr1	111210552	111210667	E070	3667
chr1	111218605	111218756	E070	11720
chr1	111218760	111218878	E070	11875
chr1	111218916	111219018	E070	12031
chr1	111235272	111235356	E070	28387
chr1	111235593	111235892	E070	28708
chr1	111176902	111176963	E071	-29922
chr1	111177051	111177994	E071	-28891
chr1	111178132	111178259	E071	-28626
chr1	111249155	111249676	E071	42270
chr1	111158236	111158697	E072	-48188
chr1	111163101	111163393	E072	-43492
chr1	111176902	111176963	E072	-29922
chr1	111177051	111177994	E072	-28891
chr1	111255744	111255892	E072	48859
chr1	111158236	111158697	E073	-48188
chr1	111163101	111163393	E073	-43492
chr1	111180776	111180994	E073	-25891
chr1	111176902	111176963	E074	-29922
chr1	111177051	111177994	E074	-28891
chr1	111255744	111255892	E074	48859
chr1	111186540	111186838	E081	-20047
chr1	111186923	111187075	E081	-19810
chr1	111205592	111205632	E081	-1253
chr1	111205917	111206156	E081	-729
chr1	111210552	111210667	E081	3667
chr1	111235272	111235356	E081	28387
chr1	111235593	111235892	E081	28708
chr1	111235972	111236022	E081	29087
chr1	111161664	111161792	E082	-45093
chr1	111163101	111163393	E082	-43492
chr1	111210552	111210667	E082	3667

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	111214433	111216291	E067	7548
chr1	111216314	111217926	E067	9429
chr1	111218095	111218575	E067	11210
chr1	111214433	111216291	E068	7548
chr1	111216314	111217926	E068	9429
chr1	111218095	111218575	E068	11210
chr1	111214433	111216291	E069	7548
chr1	111216314	111217926	E069	9429
chr1	111218095	111218575	E069	11210
chr1	111216314	111217926	E070	9429
chr1	111218095	111218575	E070	11210
chr1	111214433	111216291	E071	7548
chr1	111216314	111217926	E071	9429
chr1	111218095	111218575	E071	11210
chr1	111214433	111216291	E072	7548
chr1	111216314	111217926	E072	9429
chr1	111214433	111216291	E073	7548
chr1	111216314	111217926	E073	9429
chr1	111218095	111218575	E073	11210
chr1	111216314	111217926	E074	9429
chr1	111214433	111216291	E081	7548
chr1	111214433	111216291	E082	7548
chr1	111216314	111217926	E082	9429
chr1	111218095	111218575	E082	11210