rs2640482

Organism: Homo sapiens

Alleles: C>A

Gene : Feature

KCNA3 : Intron Variant
LOC107985174 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C==0301 (9006/29898,GnomAD)
C==0302 (8802/29118,TOPMED)
C==0347 (1739/5008,1000G)
C==0311 (1198/3854,ALSPAC)
C==0314 (1166/3708,TWINSUK)

Position: chr1:110667697 (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.110667697C>A
GRCh37.p13 chr 1	NC_000001.10:g.111210319C>A

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=0.237	A=0.763
1000Genomes	American	Sub	694	C=0.360	A=0.640
1000Genomes	East Asian	Sub	1008	C=0.436	A=0.564
1000Genomes	Europe	Sub	1006	C=0.288	A=0.712
1000Genomes	Global	Study-wide	5008	C=0.347	A=0.653
1000Genomes	South Asian	Sub	978	C=0.460	A=0.540
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.311	A=0.689
The Genome Aggregation Database	African	Sub	8716	C=0.259	A=0.741
The Genome Aggregation Database	American	Sub	838	C=0.350	A=0.650
The Genome Aggregation Database	East Asian	Sub	1608	C=0.445	A=0.555
The Genome Aggregation Database	Europe	Sub	18434	C=0.306	A=0.693
The Genome Aggregation Database	Global	Study-wide	29898	C=0.301	A=0.698
The Genome Aggregation Database	Other	Sub	302	C=0.290	A=0.710
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.302	A=0.697
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.314	A=0.686

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
rs2640482	0.00092	alcohol dependence	20201924

eQTL of rs2640482 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr1:111210319	RP11-284N8.3	ENSG00000259834.1	C>A	9.4766e-3	10657	Nucleus_accumbens_basal_ganglia

meQTL of rs2640482 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	-33356
chr1	111177051	111177994	E067	-32325
chr1	111176902	111176963	E068	-33356
chr1	111177051	111177994	E068	-32325
chr1	111180776	111180994	E068	-29325
chr1	111255744	111255892	E068	45425
chr1	111177051	111177994	E069	-32325
chr1	111255744	111255892	E069	45425
chr1	111257457	111257559	E069	47138
chr1	111161664	111161792	E070	-48527
chr1	111163101	111163393	E070	-46926
chr1	111176902	111176963	E070	-33356
chr1	111177051	111177994	E070	-32325
chr1	111178132	111178259	E070	-32060
chr1	111180776	111180994	E070	-29325
chr1	111181206	111181729	E070	-28590
chr1	111186540	111186838	E070	-23481
chr1	111186923	111187075	E070	-23244
chr1	111188000	111188238	E070	-22081
chr1	111188283	111188343	E070	-21976
chr1	111188380	111188619	E070	-21700
chr1	111210552	111210667	E070	233
chr1	111218605	111218756	E070	8286
chr1	111218760	111218878	E070	8441
chr1	111218916	111219018	E070	8597
chr1	111235272	111235356	E070	24953
chr1	111235593	111235892	E070	25274
chr1	111259934	111260024	E070	49615
chr1	111176902	111176963	E071	-33356
chr1	111177051	111177994	E071	-32325
chr1	111178132	111178259	E071	-32060
chr1	111249155	111249676	E071	38836
chr1	111257457	111257559	E071	47138
chr1	111163101	111163393	E072	-46926
chr1	111176902	111176963	E072	-33356
chr1	111177051	111177994	E072	-32325
chr1	111255744	111255892	E072	45425
chr1	111257457	111257559	E072	47138
chr1	111163101	111163393	E073	-46926
chr1	111180776	111180994	E073	-29325
chr1	111257457	111257559	E073	47138
chr1	111176902	111176963	E074	-33356
chr1	111177051	111177994	E074	-32325
chr1	111255744	111255892	E074	45425
chr1	111186540	111186838	E081	-23481
chr1	111186923	111187075	E081	-23244
chr1	111205592	111205632	E081	-4687
chr1	111205917	111206156	E081	-4163
chr1	111210552	111210667	E081	233
chr1	111235272	111235356	E081	24953
chr1	111235593	111235892	E081	25274
chr1	111235972	111236022	E081	25653
chr1	111257457	111257559	E081	47138
chr1	111161664	111161792	E082	-48527
chr1	111163101	111163393	E082	-46926
chr1	111210552	111210667	E082	233

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	111214433	111216291	E067	4114
chr1	111216314	111217926	E067	5995
chr1	111218095	111218575	E067	7776
chr1	111214433	111216291	E068	4114
chr1	111216314	111217926	E068	5995
chr1	111218095	111218575	E068	7776
chr1	111214433	111216291	E069	4114
chr1	111216314	111217926	E069	5995
chr1	111218095	111218575	E069	7776
chr1	111216314	111217926	E070	5995
chr1	111218095	111218575	E070	7776
chr1	111214433	111216291	E071	4114
chr1	111216314	111217926	E071	5995
chr1	111218095	111218575	E071	7776
chr1	111214433	111216291	E072	4114
chr1	111216314	111217926	E072	5995
chr1	111214433	111216291	E073	4114
chr1	111216314	111217926	E073	5995
chr1	111218095	111218575	E073	7776
chr1	111216314	111217926	E074	5995
chr1	111214433	111216291	E081	4114
chr1	111214433	111216291	E082	4114
chr1	111216314	111217926	E082	5995
chr1	111218095	111218575	E082	7776