rs13411251

Organism: Homo sapiens

Alleles: T>G

Gene : Feature

CAB39 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0140 (4208/29932,GnomAD)
G=0185 (5404/29118,TOPMED)
G=0154 (772/5008,1000G)
G=0074 (285/3854,ALSPAC)
G=0084 (312/3708,TWINSUK)

Position: chr2:230721625 (GRCh38.p7) (2q37.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 81 Enhancers around

Promoter: 10 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.230721625T>G
GRCh37.p13 chr 2	NC_000002.11:g.231586340T>G

Gene: CAB39, calcium binding protein 39(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CAB39 transcript variant 2	NM_001130849.1:c.	N/A	Intron Variant
CAB39 transcript variant 3	NM_001130850.1:c.	N/A	Intron Variant
CAB39 transcript variant 1	NM_016289.3:c.	N/A	Intron Variant
CAB39 transcript variant X1	XM_011511350.2:c.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.623	G=0.377
1000Genomes	American	Sub	694	T=0.910	G=0.090
1000Genomes	East Asian	Sub	1008	T=0.933	G=0.067
1000Genomes	Europe	Sub	1006	T=0.921	G=0.079
1000Genomes	Global	Study-wide	5008	T=0.846	G=0.154
1000Genomes	South Asian	Sub	978	T=0.930	G=0.070
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.926	G=0.074
The Genome Aggregation Database	African	Sub	8700	T=0.694	G=0.306
The Genome Aggregation Database	American	Sub	838	T=0.930	G=0.070
The Genome Aggregation Database	East Asian	Sub	1620	T=0.974	G=0.026
The Genome Aggregation Database	Europe	Sub	18472	T=0.923	G=0.076
The Genome Aggregation Database	Global	Study-wide	29932	T=0.859	G=0.140
The Genome Aggregation Database	Other	Sub	302	T=0.880	G=0.120
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.814	G=0.185
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.916	G=0.084

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

SNP ID	p-value	Traits	Study
rs13411251	0.00024	alcohol dependence(early age of onset)	20201924
rs13411251	0.00031	alcohol dependence	20201924

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
There is no eQTL annotation for this SNP

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	231580545	231580595	E067	-5745
chr2	231582211	231582261	E067	-4079
chr2	231582286	231582469	E067	-3871
chr2	231582481	231582658	E067	-3682
chr2	231582802	231583082	E067	-3258
chr2	231584571	231584661	E067	-1679
chr2	231584774	231584855	E067	-1485
chr2	231602916	231603530	E067	16576
chr2	231623947	231624121	E067	37607
chr2	231580545	231580595	E068	-5745
chr2	231582211	231582261	E068	-4079
chr2	231582286	231582469	E068	-3871
chr2	231582481	231582658	E068	-3682
chr2	231600670	231600765	E068	14330
chr2	231602195	231602249	E068	15855
chr2	231602514	231602906	E068	16174
chr2	231602916	231603530	E068	16576
chr2	231615732	231616286	E068	29392
chr2	231623947	231624121	E068	37607
chr2	231624214	231624407	E068	37874
chr2	231555331	231555518	E069	-30822
chr2	231580545	231580595	E069	-5745
chr2	231582286	231582469	E069	-3871
chr2	231582481	231582658	E069	-3682
chr2	231582802	231583082	E069	-3258
chr2	231602916	231603530	E069	16576
chr2	231615732	231616286	E069	29392
chr2	231623345	231623504	E069	37005
chr2	231623512	231623891	E069	37172
chr2	231623947	231624121	E069	37607
chr2	231624214	231624407	E069	37874
chr2	231580545	231580595	E070	-5745
chr2	231623947	231624121	E070	37607
chr2	231580805	231580875	E071	-5465
chr2	231582211	231582261	E071	-4079
chr2	231582286	231582469	E071	-3871
chr2	231582481	231582658	E071	-3682
chr2	231582802	231583082	E071	-3258
chr2	231602916	231603530	E071	16576
chr2	231615732	231616286	E071	29392
chr2	231616417	231616469	E071	30077
chr2	231621875	231621956	E071	35535
chr2	231622073	231622215	E071	35733
chr2	231622270	231622438	E071	35930
chr2	231629960	231630061	E071	43620
chr2	231580545	231580595	E072	-5745
chr2	231580805	231580875	E072	-5465
chr2	231582286	231582469	E072	-3871
chr2	231582481	231582658	E072	-3682
chr2	231582802	231583082	E072	-3258
chr2	231602916	231603530	E072	16576
chr2	231615732	231616286	E072	29392
chr2	231620627	231621187	E072	34287
chr2	231623512	231623891	E072	37172
chr2	231623947	231624121	E072	37607
chr2	231630275	231630623	E072	43935
chr2	231555760	231556208	E073	-30132
chr2	231580545	231580595	E073	-5745
chr2	231582211	231582261	E073	-4079
chr2	231582286	231582469	E073	-3871
chr2	231582481	231582658	E073	-3682
chr2	231617518	231617727	E073	31178
chr2	231623345	231623504	E073	37005
chr2	231623512	231623891	E073	37172
chr2	231623947	231624121	E073	37607
chr2	231624214	231624407	E073	37874
chr2	231580545	231580595	E074	-5745
chr2	231582286	231582469	E074	-3871
chr2	231582481	231582658	E074	-3682
chr2	231582802	231583082	E074	-3258
chr2	231584571	231584661	E074	-1679
chr2	231584774	231584855	E074	-1485
chr2	231602514	231602906	E074	16174
chr2	231602916	231603530	E074	16576
chr2	231615732	231616286	E074	29392
chr2	231623345	231623504	E074	37005
chr2	231623512	231623891	E074	37172
chr2	231623947	231624121	E074	37607
chr2	231555331	231555518	E081	-30822
chr2	231580545	231580595	E081	-5745
chr2	231555331	231555518	E082	-30822

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr2	231576818	231579281	E067	-7059
chr2	231576818	231579281	E068	-7059
chr2	231576818	231579281	E069	-7059
chr2	231576818	231579281	E070	-7059
chr2	231576818	231579281	E071	-7059
chr2	231576818	231579281	E072	-7059
chr2	231576818	231579281	E073	-7059
chr2	231576818	231579281	E074	-7059
chr2	231576818	231579281	E081	-7059
chr2	231576818	231579281	E082	-7059

rs13411251

Genomic Coordinates

Gene: CAB39, calcium binding protein 39(plus strand)

Population Frequency

P-Value

eQTL of rs13411251 in Brain tissues (GTEx Analysis Release V7)

meQTL of rs13411251 in Fetal Brain

Genomic View

Chromatin Interaction

Enhancer Annotation (GRCh37.p13)

Promoter Annotation (GRCh37.p13)