rs2640480

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==0320 (9592/29892,GnomAD)
C==0332 (9685/29118,TOPMED)
C==0367 (1840/5008,1000G)
C==0311 (1198/3854,ALSPAC)
C==0314 (1166/3708,TWINSUK)

Position: chr1:110670626 (GRCh38.p7) (1p13.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 2 publication(s)

Genomic View: See rs on genome

Enhancer: 52 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.110670626C>A
GRCh37.p13 chr 1	NC_000001.10:g.111213248C>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=0.308	A=0.692
1000Genomes	American	Sub	694	C=0.370	A=0.630
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=0.367	A=0.633
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	8712	C=0.326	A=0.674
The Genome Aggregation Database	American	Sub	830	C=0.360	A=0.640
The Genome Aggregation Database	East Asian	Sub	1604	C=0.446	A=0.554
The Genome Aggregation Database	Europe	Sub	18444	C=0.306	A=0.693
The Genome Aggregation Database	Global	Study-wide	29892	C=0.320	A=0.679
The Genome Aggregation Database	Other	Sub	302	C=0.290	A=0.710
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.332	A=0.667
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
22045429	Polymorphism in the KCNA3 gene is associated with susceptibility to autoimmune pancreatitis in the Japanese population.	Ota M	Dis Markers

P-Value

SNP ID	p-value	Traits	Study
rs2640480	0.00043	alcohol dependence	20201924

eQTL of rs2640480 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 rs2640480 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	-36285
chr1	111177051	111177994	E067	-35254
chr1	111176902	111176963	E068	-36285
chr1	111177051	111177994	E068	-35254
chr1	111180776	111180994	E068	-32254
chr1	111255744	111255892	E068	42496
chr1	111177051	111177994	E069	-35254
chr1	111255744	111255892	E069	42496
chr1	111257457	111257559	E069	44209
chr1	111176902	111176963	E070	-36285
chr1	111177051	111177994	E070	-35254
chr1	111178132	111178259	E070	-34989
chr1	111180776	111180994	E070	-32254
chr1	111181206	111181729	E070	-31519
chr1	111186540	111186838	E070	-26410
chr1	111186923	111187075	E070	-26173
chr1	111188000	111188238	E070	-25010
chr1	111188283	111188343	E070	-24905
chr1	111188380	111188619	E070	-24629
chr1	111210552	111210667	E070	-2581
chr1	111218605	111218756	E070	5357
chr1	111218760	111218878	E070	5512
chr1	111218916	111219018	E070	5668
chr1	111235272	111235356	E070	22024
chr1	111235593	111235892	E070	22345
chr1	111259934	111260024	E070	46686
chr1	111261245	111261316	E070	47997
chr1	111176902	111176963	E071	-36285
chr1	111177051	111177994	E071	-35254
chr1	111178132	111178259	E071	-34989
chr1	111249155	111249676	E071	35907
chr1	111257457	111257559	E071	44209
chr1	111176902	111176963	E072	-36285
chr1	111177051	111177994	E072	-35254
chr1	111255744	111255892	E072	42496
chr1	111257457	111257559	E072	44209
chr1	111180776	111180994	E073	-32254
chr1	111257457	111257559	E073	44209
chr1	111176902	111176963	E074	-36285
chr1	111177051	111177994	E074	-35254
chr1	111255744	111255892	E074	42496
chr1	111186540	111186838	E081	-26410
chr1	111186923	111187075	E081	-26173
chr1	111205592	111205632	E081	-7616
chr1	111205917	111206156	E081	-7092
chr1	111210552	111210667	E081	-2581
chr1	111235272	111235356	E081	22024
chr1	111235593	111235892	E081	22345
chr1	111235972	111236022	E081	22724
chr1	111257457	111257559	E081	44209
chr1	111261245	111261316	E081	47997
chr1	111210552	111210667	E082	-2581

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	111214433	111216291	E067	1185
chr1	111216314	111217926	E067	3066
chr1	111218095	111218575	E067	4847
chr1	111214433	111216291	E068	1185
chr1	111216314	111217926	E068	3066
chr1	111218095	111218575	E068	4847
chr1	111214433	111216291	E069	1185
chr1	111216314	111217926	E069	3066
chr1	111218095	111218575	E069	4847
chr1	111216314	111217926	E070	3066
chr1	111218095	111218575	E070	4847
chr1	111214433	111216291	E071	1185
chr1	111216314	111217926	E071	3066
chr1	111218095	111218575	E071	4847
chr1	111214433	111216291	E072	1185
chr1	111216314	111217926	E072	3066
chr1	111214433	111216291	E073	1185
chr1	111216314	111217926	E073	3066
chr1	111218095	111218575	E073	4847
chr1	111216314	111217926	E074	3066
chr1	111214433	111216291	E081	1185
chr1	111214433	111216291	E082	1185
chr1	111216314	111217926	E082	3066
chr1	111218095	111218575	E082	4847