rs3792068

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

CAB39 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0139 (4190/29950,GnomAD)
G=0184 (5384/29118,TOPMED)
G=0155 (777/5008,1000G)
G=0073 (283/3854,ALSPAC)
G=0084 (311/3708,TWINSUK)

Position: chr2:230808510 (GRCh38.p7) (2q37.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 57 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.230808510A>G
GRCh37.p13 chr 2	NC_000002.11:g.231673225A>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

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.622	G=0.378
1000Genomes	American	Sub	694	A=0.910	G=0.090
1000Genomes	East Asian	Sub	1008	A=0.933	G=0.067
1000Genomes	Europe	Sub	1006	A=0.920	G=0.080
1000Genomes	Global	Study-wide	5008	A=0.845	G=0.155
1000Genomes	South Asian	Sub	978	A=0.930	G=0.070
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.927	G=0.073
The Genome Aggregation Database	African	Sub	8710	A=0.696	G=0.304
The Genome Aggregation Database	American	Sub	838	A=0.930	G=0.070
The Genome Aggregation Database	East Asian	Sub	1620	A=0.974	G=0.026
The Genome Aggregation Database	Europe	Sub	18480	A=0.924	G=0.076
The Genome Aggregation Database	Global	Study-wide	29950	A=0.860	G=0.139
The Genome Aggregation Database	Other	Sub	302	A=0.880	G=0.120
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.815	G=0.184
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=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

P-Value

SNP ID	p-value	Traits	Study
rs3792068	0.00034	alcohol dependence(early age of onset)	20201924
rs3792068	0.0004	alcohol dependence	20201924

eQTL of rs3792068 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 rs3792068 in Fetal Brain

Probe ID	Position	Gene	beta	p-value
cg15442058	chr2:231598059	CAB39	-0.0430576864456252	4.6693e-21

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	231623947	231624121	E067	-49104
chr2	231646016	231646656	E067	-26569
chr2	231658439	231659623	E067	-13602
chr2	231689067	231689595	E067	15842
chr2	231623947	231624121	E068	-49104
chr2	231624214	231624407	E068	-48818
chr2	231642969	231643107	E068	-30118
chr2	231643430	231643580	E068	-29645
chr2	231645875	231645935	E068	-27290
chr2	231646016	231646656	E068	-26569
chr2	231646661	231646717	E068	-26508
chr2	231649498	231650014	E068	-23211
chr2	231650166	231650351	E068	-22874
chr2	231712602	231713058	E068	39377
chr2	231713079	231713146	E068	39854
chr2	231623345	231623504	E069	-49721
chr2	231623512	231623891	E069	-49334
chr2	231623947	231624121	E069	-49104
chr2	231624214	231624407	E069	-48818
chr2	231646016	231646656	E069	-26569
chr2	231646661	231646717	E069	-26508
chr2	231623947	231624121	E070	-49104
chr2	231629960	231630061	E071	-43164
chr2	231646016	231646656	E071	-26569
chr2	231646661	231646717	E071	-26508
chr2	231658439	231659623	E071	-13602
chr2	231661131	231661202	E071	-12023
chr2	231661247	231661453	E071	-11772
chr2	231662208	231662282	E071	-10943
chr2	231662519	231662833	E071	-10392
chr2	231663101	231663196	E071	-10029
chr2	231663231	231663301	E071	-9924
chr2	231663342	231663403	E071	-9822
chr2	231689067	231689595	E071	15842
chr2	231623512	231623891	E072	-49334
chr2	231623947	231624121	E072	-49104
chr2	231630275	231630623	E072	-42602
chr2	231646016	231646656	E072	-26569
chr2	231658439	231659623	E072	-13602
chr2	231623345	231623504	E073	-49721
chr2	231623512	231623891	E073	-49334
chr2	231623947	231624121	E073	-49104
chr2	231624214	231624407	E073	-48818
chr2	231643430	231643580	E073	-29645
chr2	231689067	231689595	E073	15842
chr2	231712602	231713058	E073	39377
chr2	231713079	231713146	E073	39854
chr2	231623345	231623504	E074	-49721
chr2	231623512	231623891	E074	-49334
chr2	231623947	231624121	E074	-49104
chr2	231646016	231646656	E074	-26569
chr2	231689067	231689595	E074	15842
chr2	231658088	231658173	E081	-15052
chr2	231658439	231659623	E081	-13602
chr2	231718573	231718623	E081	45348
chr2	231688398	231688478	E082	15173
chr2	231688568	231688622	E082	15343

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr2	231692917	231693090	E068	19692
chr2	231692917	231693090	E071	19692
chr2	231692917	231693090	E082	19692
chr2	231693176	231693427	E082	19951