rs7611373

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

CNTN4 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0416 (12421/29834,GnomAD)
A=0421 (12262/29118,TOPMED)
G==0476 (2385/5008,1000G)
A=0332 (1280/3854,ALSPAC)
A=0338 (1252/3708,TWINSUK)

Position: chr3:2875753 (GRCh38.p7) (3p26.2)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 10 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.2875753G>A
GRCh37.p13 chr 3	NC_000003.11:g.2917437G>A
CNTN4 RefSeqGene	NG_012827.1:g.780191G>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 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 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=0.519	A=0.481
1000Genomes	American	Sub	694	G=0.470	A=0.530
1000Genomes	East Asian	Sub	1008	G=0.245	A=0.755
1000Genomes	Europe	Sub	1006	G=0.629	A=0.371
1000Genomes	Global	Study-wide	5008	G=0.476	A=0.524
1000Genomes	South Asian	Sub	978	G=0.500	A=0.500
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.668	A=0.332
The Genome Aggregation Database	African	Sub	8694	G=0.552	A=0.448
The Genome Aggregation Database	American	Sub	830	G=0.480	A=0.520
The Genome Aggregation Database	East Asian	Sub	1582	G=0.276	A=0.724
The Genome Aggregation Database	Europe	Sub	18430	G=0.630	A=0.369
The Genome Aggregation Database	Global	Study-wide	29834	G=0.583	A=0.416
The Genome Aggregation Database	Other	Sub	298	G=0.510	A=0.490
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.578	A=0.421
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.662	A=0.338

PMID	Title	Author	Journal
23743675	A meta-analysis of two genome-wide association studies to identify novel loci for maximum number of alcoholic drinks.	Kapoor M	Hum Genet

P-Value

SNP ID	p-value	Traits	Study
rs7611373	2.64E-05	alcohol consumption	23743675

eQTL of rs7611373 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 rs7611373 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	9053
chr3	2929326	2929382	E070	11889
chr3	2929437	2929662	E070	12000
chr3	2930138	2930611	E081	12701
chr3	2931053	2931255	E081	13616
chr3	2931424	2931663	E081	13987
chr3	2931685	2931876	E081	14248
chr3	2931053	2931255	E082	13616
chr3	2931424	2931663	E082	13987
chr3	2931685	2931876	E082	14248