rs10865016

Organism: Homo sapiens

Alleles: G>A / G>T

Gene : Feature

CNGA3 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0203 (6085/29918,GnomAD)
A=0242 (1212/5008,1000G)
A=0187 (719/3854,ALSPAC)
A=0180 (669/3708,TWINSUK)

Position: chr2:98372841 (GRCh38.p7) (2q11.2)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 11 Enhancers around

Promoter: 45 Promoters around

Molecule type	Change	Amino acid[Codon]	SO Term
CNGA3 transcript variant 2	NM_001079878.1:c.	N/A	Intron Variant
CNGA3 transcript variant 1	NM_001298.2:c.	N/A	Intron Variant
CNGA3 transcript variant X2	XM_006712243.2:c.	N/A	Intron Variant
CNGA3 transcript variant X1	XM_011510554.2:c.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.815	A=0.185
1000Genomes	American	Sub	694	G=0.620	A=0.380
1000Genomes	East Asian	Sub	1008	G=0.677	A=0.323
1000Genomes	Europe	Sub	1006	G=0.790	A=0.210
1000Genomes	Global	Study-wide	5008	G=0.758	A=0.242
1000Genomes	South Asian	Sub	978	G=0.830	A=0.170
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.813	A=0.187
The Genome Aggregation Database	African	Sub	8708	G=0.822	A=0.178
The Genome Aggregation Database	American	Sub	838	G=0.590	A=0.410
The Genome Aggregation Database	East Asian	Sub	1618	G=0.640	A=0.360
The Genome Aggregation Database	Europe	Sub	18452	G=0.809	A=0.190
The Genome Aggregation Database	Global	Study-wide	29918	G=0.796	A=0.203
The Genome Aggregation Database	Other	Sub	302	G=0.660	A=0.340
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.820	A=0.180

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

SNP ID	p-value	Traits	Study
rs10865016	9.67E-06	nicotine smoking	19268276

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
There is no eQTL annotation for this SNP

Probe ID	Position	Gene	beta	p-value
There is no meQTL annotation for this SNP

There is no significant Hi-C chromatin interaction data for this SNP.

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr2	136461024	136461125	E068	-23265
chr2	136502380	136502652	E068	17990
chr2	136502380	136502652	E069	17990
chr2	136502380	136502652	E070	17990
chr2	136502380	136502652	E071	17990
chr2	136502380	136502652	E072	17990
chr2	136447044	136447097	E074	-37293
chr2	136447109	136447189	E074	-37201
chr2	136461024	136461125	E074	-23265
chr2	136502380	136502652	E081	17990
chr2	136502380	136502652	E082	17990

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr2	136445571	136446031	E067	-38359
chr2	136446044	136446296	E067	-38094
chr2	136498730	136500727	E067	14340
chr2	136500838	136500939	E067	16448
chr2	136500984	136501080	E067	16594
chr2	136501134	136501178	E067	16744
chr2	136498730	136500727	E068	14340
chr2	136500838	136500939	E068	16448
chr2	136500984	136501080	E068	16594
chr2	136501134	136501178	E068	16744
chr2	136445571	136446031	E069	-38359
chr2	136446044	136446296	E069	-38094
chr2	136498730	136500727	E069	14340
chr2	136500838	136500939	E069	16448
chr2	136500984	136501080	E069	16594
chr2	136501134	136501178	E069	16744
chr2	136498730	136500727	E070	14340
chr2	136500838	136500939	E070	16448
chr2	136500984	136501080	E070	16594
chr2	136501134	136501178	E070	16744
chr2	136445571	136446031	E071	-38359
chr2	136446044	136446296	E071	-38094
chr2	136498730	136500727	E071	14340
chr2	136500838	136500939	E071	16448
chr2	136500984	136501080	E071	16594
chr2	136501134	136501178	E071	16744
chr2	136445571	136446031	E072	-38359
chr2	136446044	136446296	E072	-38094
chr2	136498730	136500727	E072	14340
chr2	136500838	136500939	E072	16448
chr2	136500984	136501080	E072	16594
chr2	136501134	136501178	E072	16744
chr2	136498730	136500727	E073	14340
chr2	136500838	136500939	E073	16448
chr2	136500984	136501080	E073	16594
chr2	136501134	136501178	E073	16744
chr2	136445571	136446031	E074	-38359
chr2	136498730	136500727	E074	14340
chr2	136500838	136500939	E081	16448
chr2	136500984	136501080	E081	16594
chr2	136501134	136501178	E081	16744
chr2	136498730	136500727	E082	14340
chr2	136500838	136500939	E082	16448
chr2	136500984	136501080	E082	16594
chr2	136501134	136501178	E082	16744