rs17038032

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

CNTN6 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0147 (4393/29874,GnomAD)
T=0148 (4315/29118,TOPMED)
T=0131 (657/5008,1000G)
T=0161 (621/3854,ALSPAC)
T=0163 (605/3708,TWINSUK)

Position: chr3:1347433 (GRCh38.p7) (3p26.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 2 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.1347433C>T
GRCh37.p13 chr 3	NC_000003.11:g.1389117C>T

Gene: CNTN6, contactin 6(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CNTN6 transcript variant 2	NM_001289080.1:c.	N/A	Intron Variant
CNTN6 transcript variant 3	NM_001289081.1:c.	N/A	Intron Variant
CNTN6 transcript variant 1	NM_014461.3:c.	N/A	Intron Variant
CNTN6 transcript variant X1	XM_005265058.3:c.	N/A	Intron Variant
CNTN6 transcript variant X2	XM_011533590.2:c.	N/A	Intron Variant
CNTN6 transcript variant X7	XM_011533591.2:c.	N/A	Intron Variant
CNTN6 transcript variant X1	XM_017006171.1:c.	N/A	Intron Variant
CNTN6 transcript variant X4	XM_017006172.1:c.	N/A	Intron Variant
CNTN6 transcript variant X5	XM_017006173.1:c.	N/A	Intron Variant
CNTN6 transcript variant X4	XM_017006174.1:c.	N/A	Intron Variant
CNTN6 transcript variant X8	XM_017006175.1:c.	N/A	Intron Variant
CNTN6 transcript variant X9	XM_017006176.1:c.	N/A	Intron Variant
CNTN6 transcript variant X10	XM_017006177.1:c.	N/A	Intron Variant
CNTN6 transcript variant X7	XR_940415.2:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.839	T=0.161
1000Genomes	American	Sub	694	C=0.890	T=0.110
1000Genomes	East Asian	Sub	1008	C=0.929	T=0.071
1000Genomes	Europe	Sub	1006	C=0.863	T=0.137
1000Genomes	Global	Study-wide	5008	C=0.869	T=0.131
1000Genomes	South Asian	Sub	978	C=0.840	T=0.160
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.839	T=0.161
The Genome Aggregation Database	African	Sub	8718	C=0.843	T=0.157
The Genome Aggregation Database	American	Sub	834	C=0.880	T=0.120
The Genome Aggregation Database	East Asian	Sub	1580	C=0.937	T=0.063
The Genome Aggregation Database	Europe	Sub	18440	C=0.849	T=0.151
The Genome Aggregation Database	Global	Study-wide	29874	C=0.852	T=0.147
The Genome Aggregation Database	Other	Sub	302	C=0.870	T=0.130
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.851	T=0.148
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.837	T=0.163

PMID	Title	Author	Journal
21314694	Genomewide association analysis of symptoms of alcohol dependence in the molecular genetics of schizophrenia (MGS2) control sample.	Kendler KS	Alcohol Clin Exp Res

P-Value

SNP ID	p-value	Traits	Study
rs17038032	0.000811	alcohol dependence	21314694

eQTL of rs17038032 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 rs17038032 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	1422804	1422878	E070	33687
chr3	1422995	1423231	E070	33878