rs10933355

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

CAB39 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0140 (4202/29952,GnomAD)
A=0185 (5391/29118,TOPMED)
A=0155 (778/5008,1000G)
A=0074 (285/3854,ALSPAC)
A=0084 (313/3708,TWINSUK)

Position: chr2:230717481 (GRCh38.p7) (2q37.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 84 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.230717481G>A
GRCh37.p13 chr 2	NC_000002.11:g.231582196G>A

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

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.620	A=0.380
1000Genomes	American	Sub	694	G=0.910	A=0.090
1000Genomes	East Asian	Sub	1008	G=0.933	A=0.067
1000Genomes	Europe	Sub	1006	G=0.920	A=0.080
1000Genomes	Global	Study-wide	5008	G=0.845	A=0.155
1000Genomes	South Asian	Sub	978	G=0.930	A=0.070
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.926	A=0.074
The Genome Aggregation Database	African	Sub	8700	G=0.694	A=0.306
The Genome Aggregation Database	American	Sub	838	G=0.930	A=0.070
The Genome Aggregation Database	East Asian	Sub	1620	G=0.974	A=0.026
The Genome Aggregation Database	Europe	Sub	18492	G=0.924	A=0.075
The Genome Aggregation Database	Global	Study-wide	29952	G=0.859	A=0.140
The Genome Aggregation Database	Other	Sub	302	G=0.880	A=0.120
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.814	A=0.185
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.916	A=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

P-Value

SNP ID	p-value	Traits	Study
rs10933355	0.00031	alcohol dependence(early age of onset)	20201924
rs10933355	0.00037	alcohol dependence	20201924

eQTL of rs10933355 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 rs10933355 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	231580545	231580595	E067	-1601
chr2	231582211	231582261	E067	15
chr2	231582286	231582469	E067	90
chr2	231582481	231582658	E067	285
chr2	231582802	231583082	E067	606
chr2	231584571	231584661	E067	2375
chr2	231584774	231584855	E067	2578
chr2	231602916	231603530	E067	20720
chr2	231623947	231624121	E067	41751
chr2	231580545	231580595	E068	-1601
chr2	231582211	231582261	E068	15
chr2	231582286	231582469	E068	90
chr2	231582481	231582658	E068	285
chr2	231600670	231600765	E068	18474
chr2	231602195	231602249	E068	19999
chr2	231602514	231602906	E068	20318
chr2	231602916	231603530	E068	20720
chr2	231615732	231616286	E068	33536
chr2	231623947	231624121	E068	41751
chr2	231624214	231624407	E068	42018
chr2	231555331	231555518	E069	-26678
chr2	231580545	231580595	E069	-1601
chr2	231582286	231582469	E069	90
chr2	231582481	231582658	E069	285
chr2	231582802	231583082	E069	606
chr2	231602916	231603530	E069	20720
chr2	231615732	231616286	E069	33536
chr2	231623345	231623504	E069	41149
chr2	231623512	231623891	E069	41316
chr2	231623947	231624121	E069	41751
chr2	231624214	231624407	E069	42018
chr2	231580545	231580595	E070	-1601
chr2	231623947	231624121	E070	41751
chr2	231533864	231533993	E071	-48203
chr2	231534078	231534118	E071	-48078
chr2	231534180	231534340	E071	-47856
chr2	231580805	231580875	E071	-1321
chr2	231582211	231582261	E071	15
chr2	231582286	231582469	E071	90
chr2	231582481	231582658	E071	285
chr2	231582802	231583082	E071	606
chr2	231602916	231603530	E071	20720
chr2	231615732	231616286	E071	33536
chr2	231616417	231616469	E071	34221
chr2	231621875	231621956	E071	39679
chr2	231622073	231622215	E071	39877
chr2	231622270	231622438	E071	40074
chr2	231629960	231630061	E071	47764
chr2	231580545	231580595	E072	-1601
chr2	231580805	231580875	E072	-1321
chr2	231582286	231582469	E072	90
chr2	231582481	231582658	E072	285
chr2	231582802	231583082	E072	606
chr2	231602916	231603530	E072	20720
chr2	231615732	231616286	E072	33536
chr2	231620627	231621187	E072	38431
chr2	231623512	231623891	E072	41316
chr2	231623947	231624121	E072	41751
chr2	231630275	231630623	E072	48079
chr2	231555760	231556208	E073	-25988
chr2	231580545	231580595	E073	-1601
chr2	231582211	231582261	E073	15
chr2	231582286	231582469	E073	90
chr2	231582481	231582658	E073	285
chr2	231617518	231617727	E073	35322
chr2	231623345	231623504	E073	41149
chr2	231623512	231623891	E073	41316
chr2	231623947	231624121	E073	41751
chr2	231624214	231624407	E073	42018
chr2	231580545	231580595	E074	-1601
chr2	231582286	231582469	E074	90
chr2	231582481	231582658	E074	285
chr2	231582802	231583082	E074	606
chr2	231584571	231584661	E074	2375
chr2	231584774	231584855	E074	2578
chr2	231602514	231602906	E074	20318
chr2	231602916	231603530	E074	20720
chr2	231615732	231616286	E074	33536
chr2	231623345	231623504	E074	41149
chr2	231623512	231623891	E074	41316
chr2	231623947	231624121	E074	41751
chr2	231555331	231555518	E081	-26678
chr2	231580545	231580595	E081	-1601
chr2	231555331	231555518	E082	-26678

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr2	231576818	231579281	E067	-2915
chr2	231576818	231579281	E068	-2915
chr2	231576818	231579281	E069	-2915
chr2	231576818	231579281	E070	-2915
chr2	231576818	231579281	E071	-2915
chr2	231576818	231579281	E072	-2915
chr2	231576818	231579281	E073	-2915
chr2	231576818	231579281	E074	-2915
chr2	231576818	231579281	E081	-2915
chr2	231576818	231579281	E082	-2915