rs6792956

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

CNTN4 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C=0441 (13199/29882,GnomAD)
C=0460 (13414/29118,TOPMED)
C=0434 (2171/5008,1000G)
C=0447 (1721/3854,ALSPAC)
C=0432 (1603/3708,TWINSUK)

Position: chr3:2371163 (GRCh38.p7) (3p26.3)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 0 Enhancer 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.2371163T>C
GRCh37.p13 chr 3	NC_000003.11:g.2412847T>C
CNTN4 RefSeqGene	NG_012827.1:g.275601T>C

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 1	NM_175607.2:c.	N/A	Intron Variant
CNTN4 transcript variant 5	NM_001206956.1:c.	N/A	Genic Upstream Transcript Variant
CNTN4 transcript variant 3	NM_175613.2:c.	N/A	Genic Upstream Transcript 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 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 X15	XM_017005788.1:c.	N/A	Intron Variant
CNTN4 transcript variant X6	XM_011533428.2:c.	N/A	Genic Upstream Transcript Variant
CNTN4 transcript variant X8	XM_011533429.2:c.	N/A	Genic Upstream Transcript Variant
CNTN4 transcript variant X7	XM_011533430.2:c.	N/A	Genic Upstream Transcript Variant
CNTN4 transcript variant X13	XM_011533431.2:c.	N/A	Genic Upstream Transcript Variant
CNTN4 transcript variant X11	XM_017005786.1:c.	N/A	Genic Upstream Transcript Variant
CNTN4 transcript variant X12	XM_017005787.1:c.	N/A	Genic Upstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.461	C=0.539
1000Genomes	American	Sub	694	T=0.670	C=0.330
1000Genomes	East Asian	Sub	1008	T=0.605	C=0.395
1000Genomes	Europe	Sub	1006	T=0.602	C=0.398
1000Genomes	Global	Study-wide	5008	T=0.566	C=0.434
1000Genomes	South Asian	Sub	978	T=0.560	C=0.440
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.553	C=0.447
The Genome Aggregation Database	African	Sub	8692	T=0.519	C=0.481
The Genome Aggregation Database	American	Sub	828	T=0.650	C=0.350
The Genome Aggregation Database	East Asian	Sub	1610	T=0.618	C=0.382
The Genome Aggregation Database	Europe	Sub	18450	T=0.566	C=0.433
The Genome Aggregation Database	Global	Study-wide	29882	T=0.558	C=0.441
The Genome Aggregation Database	Other	Sub	302	T=0.590	C=0.410
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.539	C=0.460
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.568	C=0.432

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
rs6792956	0.000155	nicotine smoking	19268276

eQTL of rs6792956 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 rs6792956 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.