rs13423141

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

CTNNA2 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0414 (12391/29896,GnomAD)
T=0393 (11470/29116,TOPMED)
T=0419 (2098/5008,1000G)
T=0420 (1619/3854,ALSPAC)
T=0421 (1562/3708,TWINSUK)

Position: chr2:80543683 (GRCh38.p7) (2p12)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 8 Enhancers around

Promoter: 4 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.80543683C>T
GRCh37.p13 chr 2	NC_000002.11:g.80770808C>T

Gene: CTNNA2, catenin alpha 2(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CTNNA2 transcript variant 2	NM_001164883.1:c.	N/A	Intron Variant
CTNNA2 transcript variant 3	NM_001282597.2:c.	N/A	Intron Variant
CTNNA2 transcript variant 4	NM_001282598.1:c.	N/A	Intron Variant
CTNNA2 transcript variant 5	NM_001282599.1:c.	N/A	Intron Variant
CTNNA2 transcript variant 6	NM_001282600.1:c.	N/A	Intron Variant
CTNNA2 transcript variant 7	NM_001320810.1:c.	N/A	Intron Variant
CTNNA2 transcript variant 1	NM_004389.3:c.	N/A	Intron Variant
CTNNA2 transcript variant X4	XM_011532555.2:c.	N/A	Intron Variant
CTNNA2 transcript variant X2	XM_011532556.2:c.	N/A	Intron Variant
CTNNA2 transcript variant X9	XM_011532557.2:c.	N/A	Intron Variant
CTNNA2 transcript variant X3	XM_017003403.1:c.	N/A	Intron Variant
CTNNA2 transcript variant X4	XM_017003404.1:c.	N/A	Intron Variant
CTNNA2 transcript variant X5	XM_017003405.1:c.	N/A	Intron Variant
CTNNA2 transcript variant X7	XM_017003406.1:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.631	T=0.369
1000Genomes	American	Sub	694	C=0.610	T=0.390
1000Genomes	East Asian	Sub	1008	C=0.654	T=0.346
1000Genomes	Europe	Sub	1006	C=0.575	T=0.425
1000Genomes	Global	Study-wide	5008	C=0.581	T=0.419
1000Genomes	South Asian	Sub	978	C=0.420	T=0.580
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.580	T=0.420
The Genome Aggregation Database	African	Sub	8694	C=0.631	T=0.369
The Genome Aggregation Database	American	Sub	838	C=0.590	T=0.410
The Genome Aggregation Database	East Asian	Sub	1600	C=0.691	T=0.309
The Genome Aggregation Database	Europe	Sub	18462	C=0.553	T=0.446
The Genome Aggregation Database	Global	Study-wide	29896	C=0.585	T=0.414
The Genome Aggregation Database	Other	Sub	302	C=0.670	T=0.330
Trans-Omics for Precision Medicine	Global	Study-wide	29116	C=0.606	T=0.393
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.579	T=0.421

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
rs13423141	0.0000874	alcoholism	pha002891
rs13423141	0.0000874	alcohol dependence	20201924

eQTL of rs13423141 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 rs13423141 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 )
chr2	80747164	80747238	E067	-23570
chr2	80747164	80747238	E068	-23570
chr2	80746428	80746491	E069	-24317
chr2	80775702	80775926	E069	4894
chr2	80818383	80818465	E070	47575
chr2	80746428	80746491	E072	-24317
chr2	80747164	80747238	E072	-23570
chr2	80775702	80775926	E082	4894

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr2	80815940	80816430	E072	45132
chr2	80816594	80816653	E072	45786
chr2	80815940	80816430	E073	45132
chr2	80816594	80816653	E073	45786