rs7431992

Organism: Homo sapiens

Alleles: T>A

Gene : Feature

CACNA2D3 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0085 (2489/29118,TOPMED)
A=0092 (2502/27178,GnomAD)
A=0086 (429/5008,1000G)

Position: chr3:54319213 (GRCh38.p7) (3p21.1)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 70 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 3	NC_000003.12:g.54319213T>A
GRCh37.p13 chr 3	NC_000003.11:g.54353240T>A

Gene: CACNA2D3, calcium voltage-gated channel auxiliary subunit alpha2delta 3(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CACNA2D3 transcript	NM_018398.2:c.	N/A	Intron Variant
CACNA2D3 transcript variant X1	XM_005265318.2:c.	N/A	Intron Variant
CACNA2D3 transcript variant X4	XM_011533946.2:c.	N/A	Intron Variant
CACNA2D3 transcript variant X6	XM_011533947.2:c.	N/A	Intron Variant
CACNA2D3 transcript variant X9	XM_011533948.2:c.	N/A	Intron Variant
CACNA2D3 transcript variant X12	XM_011533949.2:c.	N/A	Intron Variant
CACNA2D3 transcript variant X15	XM_011533950.2:c.	N/A	Intron Variant
CACNA2D3 transcript variant X18	XM_011533951.2:c.	N/A	Intron Variant
CACNA2D3 transcript variant X19	XM_011533952.2:c.	N/A	Intron Variant
CACNA2D3 transcript variant X20	XM_011533953.2:c.	N/A	Intron Variant
CACNA2D3 transcript variant X2	XM_017006850.1:c.	N/A	Intron Variant
CACNA2D3 transcript variant X11	XM_017006852.1:c.	N/A	Intron Variant
CACNA2D3 transcript variant X21	XM_011533954.2:c.	N/A	Genic Upstream Transcript Variant
CACNA2D3 transcript variant X23	XM_011533955.1:c.	N/A	Genic Upstream Transcript Variant
CACNA2D3 transcript variant X7	XM_017006851.1:c.	N/A	Genic Upstream Transcript Variant
CACNA2D3 transcript variant X13	XM_017006853.1:c.	N/A	Genic Upstream Transcript Variant
CACNA2D3 transcript variant X14	XM_017006854.1:c.	N/A	Genic Upstream Transcript Variant
CACNA2D3 transcript variant X16	XR_001740203.1:n.	N/A	Intron Variant
CACNA2D3 transcript variant X17	XR_001740204.1:n.	N/A	Intron Variant
CACNA2D3 transcript variant X22	XR_001740205.1:n.	N/A	Intron Variant
CACNA2D3 transcript variant X5	XR_427281.2:n.	N/A	Intron Variant
CACNA2D3 transcript variant X3	XR_940472.2:n.	N/A	Intron Variant
CACNA2D3 transcript variant X9	XR_940473.2:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.955	A=0.045
1000Genomes	American	Sub	694	T=0.920	A=0.080
1000Genomes	East Asian	Sub	1008	T=0.909	A=0.091
1000Genomes	Europe	Sub	1006	T=0.879	A=0.121
1000Genomes	Global	Study-wide	5008	T=0.914	A=0.086
1000Genomes	South Asian	Sub	978	T=0.900	A=0.100
The Genome Aggregation Database	African	Sub	7704	T=0.937	A=0.063
The Genome Aggregation Database	American	Sub	752	T=0.930	A=0.070
The Genome Aggregation Database	East Asian	Sub	1474	T=0.918	A=0.082
The Genome Aggregation Database	Europe	Sub	16960	T=0.894	A=0.105
The Genome Aggregation Database	Global	Study-wide	27178	T=0.907	A=0.092
The Genome Aggregation Database	Other	Sub	288	T=0.840	A=0.160
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.914	A=0.085

PMID	Title	Author	Journal
19268276	Genome-wide association study of smoking initiation and current smoking.	Vink JM	Am J Hum Genet

P-Value

SNP ID	p-value	Traits	Study
rs7431992	0.000262	nicotine smoking	19268276

eQTL of rs7431992 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 rs7431992 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 )
chr3	54390382	54390780	E067	37142
chr3	54390863	54390973	E067	37623
chr3	54393627	54393727	E067	40387
chr3	54387781	54387859	E068	34541
chr3	54388516	54388591	E068	35276
chr3	54390026	54390129	E068	36786
chr3	54390214	54390341	E068	36974
chr3	54390382	54390780	E068	37142
chr3	54390863	54390973	E068	37623
chr3	54388774	54388834	E069	35534
chr3	54388849	54388931	E069	35609
chr3	54389275	54389332	E069	36035
chr3	54390382	54390780	E069	37142
chr3	54390863	54390973	E069	37623
chr3	54304717	54305280	E070	-47960
chr3	54305306	54305438	E070	-47802
chr3	54330712	54330773	E070	-22467
chr3	54330942	54331228	E070	-22012
chr3	54338191	54338280	E070	-14960
chr3	54338705	54338747	E070	-14493
chr3	54338999	54339142	E070	-14098
chr3	54341529	54341620	E070	-11620
chr3	54341690	54341855	E070	-11385
chr3	54364806	54364856	E070	11566
chr3	54365427	54365708	E070	12187
chr3	54366577	54366659	E070	13337
chr3	54391466	54391560	E070	38226
chr3	54338191	54338280	E071	-14960
chr3	54338705	54338747	E071	-14493
chr3	54338999	54339142	E071	-14098
chr3	54389275	54389332	E071	36035
chr3	54338191	54338280	E072	-14960
chr3	54338705	54338747	E072	-14493
chr3	54303968	54304266	E073	-48974
chr3	54305306	54305438	E073	-47802
chr3	54338191	54338280	E073	-14960
chr3	54388774	54388834	E073	35534
chr3	54388849	54388931	E073	35609
chr3	54389275	54389332	E073	36035
chr3	54390026	54390129	E073	36786
chr3	54390214	54390341	E073	36974
chr3	54390382	54390780	E073	37142
chr3	54390863	54390973	E073	37623
chr3	54304717	54305280	E081	-47960
chr3	54305306	54305438	E081	-47802
chr3	54346176	54346890	E081	-6350
chr3	54356022	54356339	E081	2782
chr3	54356377	54356710	E081	3137
chr3	54363883	54364327	E081	10643
chr3	54364806	54364856	E081	11566
chr3	54365427	54365708	E081	12187
chr3	54366577	54366659	E081	13337
chr3	54387781	54387859	E081	34541
chr3	54388050	54388105	E081	34810
chr3	54388115	54388260	E081	34875
chr3	54388516	54388591	E081	35276
chr3	54388774	54388834	E081	35534
chr3	54388849	54388931	E081	35609
chr3	54389275	54389332	E081	36035
chr3	54390026	54390129	E081	36786
chr3	54390214	54390341	E081	36974
chr3	54390382	54390780	E081	37142
chr3	54390863	54390973	E081	37623
chr3	54391466	54391560	E081	38226
chr3	54401022	54401160	E081	47782
chr3	54304717	54305280	E082	-47960
chr3	54305306	54305438	E082	-47802
chr3	54364806	54364856	E082	11566
chr3	54366577	54366659	E082	13337
chr3	54383271	54383544	E082	30031