rs1479540

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

CNTN4 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0279 (8343/29866,GnomAD)
G=0351 (10233/29118,TOPMED)
G=0428 (2141/5008,1000G)
G=0131 (505/3854,ALSPAC)
G=0124 (458/3708,TWINSUK)

Position: chr3:2587793 (GRCh38.p7) (3p26.3)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 15 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.2587793A>G
GRCh37.p13 chr 3	NC_000003.11:g.2629477A>G
CNTN4 RefSeqGene	NG_012827.1:g.492231A>G

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 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 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
CNTN4 transcript variant X13	XM_011533431.2:c.	N/A	Genic Upstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.346	G=0.654
1000Genomes	American	Sub	694	A=0.620	G=0.380
1000Genomes	East Asian	Sub	1008	A=0.579	G=0.421
1000Genomes	Europe	Sub	1006	A=0.864	G=0.136
1000Genomes	Global	Study-wide	5008	A=0.572	G=0.428
1000Genomes	South Asian	Sub	978	A=0.540	G=0.460
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.869	G=0.131
The Genome Aggregation Database	African	Sub	8698	A=0.434	G=0.566
The Genome Aggregation Database	American	Sub	832	A=0.680	G=0.320
The Genome Aggregation Database	East Asian	Sub	1612	A=0.588	G=0.412
The Genome Aggregation Database	Europe	Sub	18426	A=0.868	G=0.131
The Genome Aggregation Database	Global	Study-wide	29866	A=0.720	G=0.279
The Genome Aggregation Database	Other	Sub	298	A=0.790	G=0.210
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.648	G=0.351
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.876	G=0.124

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
rs1479540	0.000174	nicotine smoking	19268276

eQTL of rs1479540 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 rs1479540 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	2610944	2611042	E070	-18435
chr3	2600443	2600933	E081	-28544
chr3	2618932	2619001	E081	-10476
chr3	2619118	2619801	E081	-9676
chr3	2619958	2620056	E081	-9421
chr3	2620635	2620718	E081	-8759
chr3	2621576	2621782	E081	-7695
chr3	2621838	2622247	E081	-7230
chr3	2623892	2624101	E081	-5376
chr3	2598982	2599039	E082	-30438
chr3	2600443	2600933	E082	-28544
chr3	2618932	2619001	E082	-10476
chr3	2619118	2619801	E082	-9676
chr3	2620635	2620718	E082	-8759
chr3	2621576	2621782	E082	-7695