rs2441997

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

CNTLN : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G==0079 (2392/29942,GnomAD)
G==0126 (3671/29118,TOPMED)
G==0085 (426/5008,1000G)
G==0000 (1/3854,ALSPAC)
G==0000 (0/3708,TWINSUK)

Position: chr9:17474087 (GRCh38.p7) (9p22.2)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 5 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 9	NC_000009.12:g.17474087G>A
GRCh37.p13 chr 9	NC_000009.11:g.17474085G>A

Gene: CNTLN, centlein(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CNTLN transcript variant 1	NM_017738.3:c.	N/A	Intron Variant
CNTLN transcript variant 2	NM_001114395.2:c.	N/A	Genic Downstream Transcript Variant
CNTLN transcript variant 3	NM_001286984.1:c.	N/A	Genic Downstream Transcript Variant
CNTLN transcript variant 4	NM_001286985.1:c.	N/A	Genic Downstream Transcript Variant
CNTLN transcript variant X1	XM_005251492.1:c.	N/A	Intron Variant
CNTLN transcript variant X4	XM_006716793.3:c.	N/A	Intron Variant
CNTLN transcript variant X2	XM_017014839.1:c.	N/A	Intron Variant
CNTLN transcript variant X3	XM_017014840.1:c.	N/A	Intron Variant
CNTLN transcript variant X5	XM_017014841.1:c.	N/A	Intron Variant
CNTLN transcript variant X11	XM_017014844.1:c.	N/A	Intron Variant
CNTLN transcript variant X11	XM_017014845.1:c.	N/A	Intron Variant
CNTLN transcript variant X13	XM_017014846.1:c.	N/A	Intron Variant
CNTLN transcript variant X13	XM_017014847.1:c.	N/A	Intron Variant
CNTLN transcript variant X7	XM_011517941.2:c.	N/A	Genic Downstream Transcript Variant
CNTLN transcript variant X8	XM_017014842.1:c.	N/A	Genic Downstream Transcript Variant
CNTLN transcript variant X9	XM_017014843.1:c.	N/A	Genic Downstream Transcript Variant
CNTLN transcript variant X10	XR_929282.2:n.	N/A	Genic Downstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.309	A=0.691
1000Genomes	American	Sub	694	G=0.020	A=0.980
1000Genomes	East Asian	Sub	1008	G=0.000	A=1.000
1000Genomes	Europe	Sub	1006	G=0.001	A=0.999
1000Genomes	Global	Study-wide	5008	G=0.085	A=0.915
1000Genomes	South Asian	Sub	978	G=0.000	A=1.000
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.000	A=1.000
The Genome Aggregation Database	African	Sub	8692	G=0.273	A=0.727
The Genome Aggregation Database	American	Sub	838	G=0.020	A=0.980
The Genome Aggregation Database	East Asian	Sub	1622	G=0.000	A=1.000
The Genome Aggregation Database	Europe	Sub	18488	G=0.000	A=0.999
The Genome Aggregation Database	Global	Study-wide	29942	G=0.079	A=0.920
The Genome Aggregation Database	Other	Sub	302	G=0.000	A=1.000
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.126	A=0.873
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.000	A=1.000

PMID	Title	Author	Journal
20201924	Genome-wide association study of alcohol dependence implicates a region on chromosome 11.	Edenberg HJ	Alcohol Clin Exp Res

P-Value

SNP ID	p-value	Traits	Study
rs2441997	0.000419	alcohol dependence	20201924

eQTL of rs2441997 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 rs2441997 in Fetal Brain

Probe ID	Position	Gene	beta	p-value
cg02189017	chr7:158933456	VIPR2	-0.0496408757797618	6.0805e-9

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 )
chr9	17478929	17478979	E070	4844
chr9	17478984	17479086	E070	4899
chr9	17520230	17520288	E073	46145
chr9	17520379	17520904	E073	46294
chr9	17520379	17520904	E081	46294