rs3749317

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

VPRBP : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C=0068 (2051/29972,GnomAD)
C=0080 (2355/29118,TOPMED)
C=0147 (734/5008,1000G)
C=0019 (75/3854,ALSPAC)
C=0014 (53/3708,TWINSUK)

Position: chr3:51419581 (GRCh38.p7) (3p21.2)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 3 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 3	NC_000003.12:g.51419581T>C
GRCh37.p13 chr 3 fix patch HG186_PATCH	NW_003315910.1:g.40904T>C
GRCh37.p13 chr 3	NC_000003.11:g.51457035T>C

Gene: VPRBP, Vpr (HIV-1) binding protein(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
DCAF1 transcript variant 2	NM_001171904.1:c.	N/A	Intron Variant
DCAF1 transcript variant 1	NM_014703.2:c.	N/A	Intron Variant
VPRBP transcript variant X10	XM_005276753.4:c.	N/A	Intron Variant
VPRBP transcript variant X9	XM_005276755.4:c.	N/A	Intron Variant
VPRBP transcript variant X3	XM_011534273.2:c.	N/A	Intron Variant
VPRBP transcript variant X2	XM_011534274.2:c.	N/A	Intron Variant
VPRBP transcript variant X7	XM_011534275.2:c.	N/A	Intron Variant
VPRBP transcript variant X6	XM_011534276.2:c.	N/A	Intron Variant
VPRBP transcript variant X1	XM_011534277.2:c.	N/A	Intron Variant
VPRBP transcript variant X4	XM_017007546.1:c.	N/A	Intron Variant
VPRBP transcript variant X5	XM_017007547.1:c.	N/A	Intron Variant
VPRBP transcript variant X8	XM_017007548.1:c.	N/A	Intron Variant
VPRBP transcript variant X11	XM_017007549.1:c.	N/A	Intron Variant
VPRBP transcript variant X12	XM_017007550.1:c.	N/A	Intron Variant
VPRBP transcript variant X16	XM_017007551.1:c.	N/A	Intron Variant
VPRBP transcript variant X13	XR_001740385.1:n.	N/A	Intron Variant
VPRBP transcript variant X14	XR_001740386.1:n.	N/A	Intron Variant
VPRBP transcript variant X15	XR_001740387.1:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.890	C=0.110
1000Genomes	American	Sub	694	T=0.760	C=0.240
1000Genomes	East Asian	Sub	1008	T=0.647	C=0.353
1000Genomes	Europe	Sub	1006	T=0.980	C=0.020
1000Genomes	Global	Study-wide	5008	T=0.853	C=0.147
1000Genomes	South Asian	Sub	978	T=0.960	C=0.040
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.981	C=0.019
The Genome Aggregation Database	African	Sub	8722	T=0.912	C=0.088
The Genome Aggregation Database	American	Sub	836	T=0.640	C=0.360
The Genome Aggregation Database	East Asian	Sub	1620	T=0.660	C=0.340
The Genome Aggregation Database	Europe	Sub	18492	T=0.977	C=0.023
The Genome Aggregation Database	Global	Study-wide	29972	T=0.931	C=0.068
The Genome Aggregation Database	Other	Sub	302	T=0.980	C=0.020
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.919	C=0.080
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.986	C=0.014

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
rs3749317	0.000201	alcohol dependence	20201924

eQTL of rs3749317 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 rs3749317 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 )
chr3	84315	84369	E081	43411
chr3	86105	86168	E081	45201
chr3	84315	84369	E082	43411