rs1319782

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==0327 (9802/29954,GnomAD)
C==0342 (9958/29118,TOPMED)
C==0372 (1865/5008,1000G)
C==0311 (1198/3854,ALSPAC)
C==0315 (1167/3708,TWINSUK)

Position: chr1:110668911 (GRCh38.p7) (1p13.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 2 publication(s)

Genomic View: See rs on genome

Enhancer: 58 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.110668911C>T
GRCh37.p13 chr 1	NC_000001.10:g.111211533C>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=0.326	T=0.674
1000Genomes	American	Sub	694	C=0.370	T=0.630
1000Genomes	East Asian	Sub	1008	C=0.437	T=0.563
1000Genomes	Europe	Sub	1006	C=0.288	T=0.712
1000Genomes	Global	Study-wide	5008	C=0.372	T=0.628
1000Genomes	South Asian	Sub	978	C=0.460	T=0.540
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.311	T=0.689
The Genome Aggregation Database	African	Sub	8714	C=0.346	T=0.654
The Genome Aggregation Database	American	Sub	838	C=0.360	T=0.640
The Genome Aggregation Database	East Asian	Sub	1616	C=0.448	T=0.552
The Genome Aggregation Database	Europe	Sub	18484	C=0.306	T=0.693
The Genome Aggregation Database	Global	Study-wide	29954	C=0.327	T=0.672
The Genome Aggregation Database	Other	Sub	302	C=0.290	T=0.710
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.342	T=0.658
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.315	T=0.685

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
rs1319782	0.00086	alcohol dependence	20201924

eQTL of rs1319782 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 rs1319782 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	-34570
chr1	111177051	111177994	E067	-33539
chr1	111176902	111176963	E068	-34570
chr1	111177051	111177994	E068	-33539
chr1	111180776	111180994	E068	-30539
chr1	111255744	111255892	E068	44211
chr1	111177051	111177994	E069	-33539
chr1	111255744	111255892	E069	44211
chr1	111257457	111257559	E069	45924
chr1	111161664	111161792	E070	-49741
chr1	111163101	111163393	E070	-48140
chr1	111176902	111176963	E070	-34570
chr1	111177051	111177994	E070	-33539
chr1	111178132	111178259	E070	-33274
chr1	111180776	111180994	E070	-30539
chr1	111181206	111181729	E070	-29804
chr1	111186540	111186838	E070	-24695
chr1	111186923	111187075	E070	-24458
chr1	111188000	111188238	E070	-23295
chr1	111188283	111188343	E070	-23190
chr1	111188380	111188619	E070	-22914
chr1	111210552	111210667	E070	-866
chr1	111218605	111218756	E070	7072
chr1	111218760	111218878	E070	7227
chr1	111218916	111219018	E070	7383
chr1	111235272	111235356	E070	23739
chr1	111235593	111235892	E070	24060
chr1	111259934	111260024	E070	48401
chr1	111261245	111261316	E070	49712
chr1	111176902	111176963	E071	-34570
chr1	111177051	111177994	E071	-33539
chr1	111178132	111178259	E071	-33274
chr1	111249155	111249676	E071	37622
chr1	111257457	111257559	E071	45924
chr1	111163101	111163393	E072	-48140
chr1	111176902	111176963	E072	-34570
chr1	111177051	111177994	E072	-33539
chr1	111255744	111255892	E072	44211
chr1	111257457	111257559	E072	45924
chr1	111163101	111163393	E073	-48140
chr1	111180776	111180994	E073	-30539
chr1	111257457	111257559	E073	45924
chr1	111176902	111176963	E074	-34570
chr1	111177051	111177994	E074	-33539
chr1	111255744	111255892	E074	44211
chr1	111186540	111186838	E081	-24695
chr1	111186923	111187075	E081	-24458
chr1	111205592	111205632	E081	-5901
chr1	111205917	111206156	E081	-5377
chr1	111210552	111210667	E081	-866
chr1	111235272	111235356	E081	23739
chr1	111235593	111235892	E081	24060
chr1	111235972	111236022	E081	24439
chr1	111257457	111257559	E081	45924
chr1	111261245	111261316	E081	49712
chr1	111161664	111161792	E082	-49741
chr1	111163101	111163393	E082	-48140
chr1	111210552	111210667	E082	-866

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	111214433	111216291	E067	2900
chr1	111216314	111217926	E067	4781
chr1	111218095	111218575	E067	6562
chr1	111214433	111216291	E068	2900
chr1	111216314	111217926	E068	4781
chr1	111218095	111218575	E068	6562
chr1	111214433	111216291	E069	2900
chr1	111216314	111217926	E069	4781
chr1	111218095	111218575	E069	6562
chr1	111216314	111217926	E070	4781
chr1	111218095	111218575	E070	6562
chr1	111214433	111216291	E071	2900
chr1	111216314	111217926	E071	4781
chr1	111218095	111218575	E071	6562
chr1	111214433	111216291	E072	2900
chr1	111216314	111217926	E072	4781
chr1	111214433	111216291	E073	2900
chr1	111216314	111217926	E073	4781
chr1	111218095	111218575	E073	6562
chr1	111216314	111217926	E074	4781
chr1	111214433	111216291	E081	2900
chr1	111214433	111216291	E082	2900
chr1	111216314	111217926	E082	4781
chr1	111218095	111218575	E082	6562