rs17022006

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

CNTN4 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0299 (8916/29754,GnomAD)
A=0257 (7495/29118,TOPMED)
A=0345 (1729/5008,1000G)
A=0333 (1283/3854,ALSPAC)
A=0330 (1222/3708,TWINSUK)

Position: chr3:2897050 (GRCh38.p7) (3p26.2)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 11 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.2897050G>A
GRCh37.p13 chr 3	NC_000003.11:g.2938734G>A
CNTN4 RefSeqGene	NG_012827.1:g.801488G>A

Gene: CNTN4, contactin 4(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CNTN4 transcript variant 4	NM_001206955.1:c.	N/A	Intron Variant
CNTN4 transcript variant 5	NM_001206956.1:c.	N/A	Intron Variant
CNTN4 transcript variant 1	NM_175607.2:c.	N/A	Intron Variant
CNTN4 transcript variant 3	NM_175613.2:c.	N/A	Intron Variant
CNTN4 transcript variant X11	XM_006713004.3:c.	N/A	Intron Variant
CNTN4 transcript variant X2	XM_011533425.2:c.	N/A	Intron Variant
CNTN4 transcript variant X4	XM_011533426.2:c.	N/A	Intron Variant
CNTN4 transcript variant X4	XM_011533427.2:c.	N/A	Intron Variant
CNTN4 transcript variant X6	XM_011533428.2:c.	N/A	Intron Variant
CNTN4 transcript variant X8	XM_011533429.2:c.	N/A	Intron Variant
CNTN4 transcript variant X7	XM_011533430.2:c.	N/A	Intron Variant
CNTN4 transcript variant X13	XM_011533431.2:c.	N/A	Intron Variant
CNTN4 transcript variant X1	XM_017005782.1:c.	N/A	Intron Variant
CNTN4 transcript variant X3	XM_017005783.1:c.	N/A	Intron Variant
CNTN4 transcript variant X6	XM_017005784.1:c.	N/A	Intron Variant
CNTN4 transcript variant X9	XM_017005785.1:c.	N/A	Intron Variant
CNTN4 transcript variant X11	XM_017005786.1:c.	N/A	Intron Variant
CNTN4 transcript variant X12	XM_017005787.1:c.	N/A	Intron Variant
CNTN4 transcript variant X15	XM_017005788.1:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.899	A=0.101
1000Genomes	American	Sub	694	G=0.590	A=0.410
1000Genomes	East Asian	Sub	1008	G=0.410	A=0.590
1000Genomes	Europe	Sub	1006	G=0.690	A=0.310
1000Genomes	Global	Study-wide	5008	G=0.655	A=0.345
1000Genomes	South Asian	Sub	978	G=0.580	A=0.420
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.667	A=0.333
The Genome Aggregation Database	African	Sub	8688	G=0.858	A=0.142
The Genome Aggregation Database	American	Sub	826	G=0.570	A=0.430
The Genome Aggregation Database	East Asian	Sub	1600	G=0.438	A=0.562
The Genome Aggregation Database	Europe	Sub	18338	G=0.656	A=0.343
The Genome Aggregation Database	Global	Study-wide	29754	G=0.700	A=0.299
The Genome Aggregation Database	Other	Sub	302	G=0.570	A=0.430
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.742	A=0.257
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.670	A=0.330

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
rs17022006	0.000138	nicotine smoking	19268276

eQTL of rs17022006 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 rs17022006 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	2926490	2926620	E070	-12114
chr3	2929326	2929382	E070	-9352
chr3	2929437	2929662	E070	-9072
chr3	2976161	2976374	E070	37427
chr3	2930138	2930611	E081	-8123
chr3	2931053	2931255	E081	-7479
chr3	2931424	2931663	E081	-7071
chr3	2931685	2931876	E081	-6858
chr3	2931053	2931255	E082	-7479
chr3	2931424	2931663	E082	-7071
chr3	2931685	2931876	E082	-6858