rs3782886

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

BRAP : Missense Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C=0017 (2088/121356,ExAC)
C=0014 (441/29994,GnomAD)
C=0000 (8/29118,TOPMED)
T==0000 (2/13006,GO-ESP)
C=0036 (178/5008,1000G)
C=0001 (4/3854,ALSPAC)
C=0000 (0/3708,TWINSUK)

Position: chr12:111672685 (GRCh38.p7) (12q24.12)

Phenotype: AD

Dataset:

GWASdb2

Publications: 9 publication(s)

Genomic View: See rs on genome

Enhancer: 140 Enhancers around

Promoter: 10 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 12	NC_000012.12:g.111672685T>C
GRCh37.p13 chr 12	NC_000012.11:g.112110489T>C

Gene: BRAP, BRCA1 associated protein(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
BRAP transcript	NM_006768.4:c.723A>G	R [AGA]> R [AGG]	Coding Sequence Variant
BRCA1-associated protein	NP_006759.3:p.Arg...NP_006759.3:p.Arg241=	R [Arg]> R [Arg]	Synonymous Variant
BRAP transcript variant X1	XM_005253944.4:c....XM_005253944.4:c.846A>G	R [AGA]> R [AGG]	Coding Sequence Variant
BRCA1-associated protein isoform X1	XP_005254001.1:p....XP_005254001.1:p.Arg282=	R [Arg]> R [Arg]	Synonymous Variant
BRAP transcript variant X2	XM_017019992.1:c....XM_017019992.1:c.561A>G	R [AGA]> R [AGG]	Coding Sequence Variant
BRCA1-associated protein isoform X2	XP_016875481.1:p....XP_016875481.1:p.Arg187=	R [Arg]> R [Arg]	Synonymous Variant
BRAP transcript variant X3	XM_017019993.1:c....XM_017019993.1:c.276A>G	R [AGA]> R [AGG]	Coding Sequence Variant
BRCA1-associated protein isoform X3	XP_016875482.1:p....XP_016875482.1:p.Arg92=	R [Arg]> R [Arg]	Synonymous Variant
BRAP transcript variant X4	XM_017019994.1:c....XM_017019994.1:c.276A>G	R [AGA]> R [AGG]	Coding Sequence Variant
BRCA1-associated protein isoform X3	XP_016875483.1:p....XP_016875483.1:p.Arg92=	R [Arg]> R [Arg]	Synonymous Variant
BRAP transcript variant X5	XM_017019995.1:c....XM_017019995.1:c.276A>G	R [AGA]> R [AGG]	Coding Sequence Variant
BRCA1-associated protein isoform X3	XP_016875484.1:p....XP_016875484.1:p.Arg92=	R [Arg]> R [Arg]	Synonymous Variant
BRAP transcript variant X6	XM_011538789.2:c....XM_011538789.2:c.11A>G	E [GAG]> G [GGG]	Coding Sequence Variant
BRCA1-associated protein isoform X4	XP_011537091.1:p....XP_011537091.1:p.Glu4Gly	E [Glu]> G [Gly]	Missense Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=1.000	C=0.000
1000Genomes	American	Sub	694	T=1.000	C=0.000
1000Genomes	East Asian	Sub	1008	T=0.825	C=0.175
1000Genomes	Europe	Sub	1006	T=1.000	C=0.000
1000Genomes	Global	Study-wide	5008	T=0.964	C=0.036
1000Genomes	South Asian	Sub	978	T=1.000	C=0.000
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.999	C=0.001
The Exome Aggregation Consortium	American	Sub	21972	T=0.999	C=0.000
The Exome Aggregation Consortium	Asian	Sub	25148	T=0.917	C=0.082
The Exome Aggregation Consortium	Europe	Sub	73330	T=0.999	C=0.000
The Exome Aggregation Consortium	Global	Study-wide	121356	T=0.982	C=0.017
The Exome Aggregation Consortium	Other	Sub	906	T=1.000	C=0.000
The Genome Aggregation Database	African	Sub	8728	T=1.000	C=0.000
The Genome Aggregation Database	American	Sub	838	T=1.000	C=0.000
The Genome Aggregation Database	East Asian	Sub	1616	T=0.729	C=0.271
The Genome Aggregation Database	Europe	Sub	18510	T=0.999	C=0.000
The Genome Aggregation Database	Global	Study-wide	29994	T=0.985	C=0.014
The Genome Aggregation Database	Other	Sub	302	T=1.000	C=0.000
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.999	C=0.000
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=1.000	C=0.000

PMID	Title	Author	Journal
27181629	Identification of rs671, a common variant of ALDH2, as a gout susceptibility locus.	Sakiyama M	Sci Rep
24916648	A genome-wide association study identifies PLCL2 and AP3D1-DOT1L-SF3A2 as new susceptibility loci for myocardial infarction in Japanese.	Hirokawa M	Eur J Hum Genet
22965072	The single nucleotide polymorphisms in BRAP decrease the risk of metabolic syndrome in a Chinese young adult population.	Wu L	Diab Vasc Dis Res
20729852	A shared susceptibility locus in PLCE1 at 10q23 for gastric adenocarcinoma and esophageal squamous cell carcinoma.	Abnet CC	Nat Genet
24277619	ALDH2 is associated to alcohol dependence and is the major genetic determinant of "daily maximum drinks" in a GWAS study of an isolated rural Chinese sample.	Quillen EE	Am J Med Genet B Neuropsychiatr Genet
23555315	Genome-wide testing of putative functional exonic variants in relationship with breast and prostate cancer risk in a multiethnic population.	Haiman CA	PLoS Genet
27245511	Effect of dietary energy and polymorphisms in BRAP and GHRL on obesity and metabolic traits.	Imaizumi T	Obes Res Clin Pract
21971053	Genome-wide association study of coronary artery disease in the Japanese.	Takeuchi F	Eur J Hum Genet
26833210	Evaluation of pleiotropic effects among common genetic loci identified for cardio-metabolic traits in a Korean population.	Kim YK	Cardiovasc Diabetol

P-Value

SNP ID	p-value	Traits	Study
rs3782886	4.48E-77	alcohol (ever vs. never)	23555315
rs3782886	1.95E-16	alcohol consumption (maxi-drinks)	24277619
rs3782886	2.17E-09	alcohol consumption	23555315
rs3782886	4.55E-08	alcohol dependence	24277619

eQTL of rs3782886 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 rs3782886 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 )
chr12	112073331	112075037	E067	-35452
chr12	112080293	112080437	E067	-30052
chr12	112080574	112080753	E067	-29736
chr12	112080875	112082060	E067	-28429
chr12	112091561	112091601	E067	-18888
chr12	112103505	112103591	E067	-6898
chr12	112121005	112121049	E067	10516
chr12	112121293	112121343	E067	10804
chr12	112121582	112121632	E067	11093
chr12	112121724	112121796	E067	11235
chr12	112121888	112121937	E067	11399
chr12	112122047	112122097	E067	11558
chr12	112122118	112122168	E067	11629
chr12	112153115	112153510	E067	42626
chr12	112153601	112153651	E067	43112
chr12	112073331	112075037	E068	-35452
chr12	112075134	112075332	E068	-35157
chr12	112075381	112075450	E068	-35039
chr12	112078196	112078770	E068	-31719
chr12	112121888	112121937	E068	11399
chr12	112122047	112122097	E068	11558
chr12	112122118	112122168	E068	11629
chr12	112125136	112125350	E068	14647
chr12	112125515	112125592	E068	15026
chr12	112152787	112153106	E068	42298
chr12	112153115	112153510	E068	42626
chr12	112153601	112153651	E068	43112
chr12	112153981	112154032	E068	43492
chr12	112073331	112075037	E069	-35452
chr12	112080293	112080437	E069	-30052
chr12	112080574	112080753	E069	-29736
chr12	112080875	112082060	E069	-28429
chr12	112082158	112082202	E069	-28287
chr12	112082262	112082349	E069	-28140
chr12	112091561	112091601	E069	-18888
chr12	112091859	112091917	E069	-18572
chr12	112091934	112092039	E069	-18450
chr12	112093805	112093855	E069	-16634
chr12	112093900	112094228	E069	-16261
chr12	112102495	112102555	E069	-7934
chr12	112102671	112102725	E069	-7764
chr12	112102766	112102816	E069	-7673
chr12	112121582	112121632	E069	11093
chr12	112121724	112121796	E069	11235
chr12	112121888	112121937	E069	11399
chr12	112122047	112122097	E069	11558
chr12	112122118	112122168	E069	11629
chr12	112125136	112125350	E069	14647
chr12	112073331	112075037	E070	-35452
chr12	112121582	112121632	E070	11093
chr12	112121724	112121796	E070	11235
chr12	112121888	112121937	E070	11399
chr12	112122047	112122097	E070	11558
chr12	112122118	112122168	E070	11629
chr12	112125136	112125350	E070	14647
chr12	112073331	112075037	E071	-35452
chr12	112080293	112080437	E071	-30052
chr12	112080574	112080753	E071	-29736
chr12	112080875	112082060	E071	-28429
chr12	112091934	112092039	E071	-18450
chr12	112093805	112093855	E071	-16634
chr12	112093900	112094228	E071	-16261
chr12	112094397	112094457	E071	-16032
chr12	112121888	112121937	E071	11399
chr12	112122047	112122097	E071	11558
chr12	112122118	112122168	E071	11629
chr12	112153115	112153510	E071	42626
chr12	112073331	112075037	E072	-35452
chr12	112080293	112080437	E072	-30052
chr12	112080574	112080753	E072	-29736
chr12	112080875	112082060	E072	-28429
chr12	112082158	112082202	E072	-28287
chr12	112091561	112091601	E072	-18888
chr12	112091859	112091917	E072	-18572
chr12	112091934	112092039	E072	-18450
chr12	112102077	112102167	E072	-8322
chr12	112102175	112102233	E072	-8256
chr12	112102495	112102555	E072	-7934
chr12	112102671	112102725	E072	-7764
chr12	112102766	112102816	E072	-7673
chr12	112102946	112103017	E072	-7472
chr12	112103068	112103233	E072	-7256
chr12	112103505	112103591	E072	-6898
chr12	112120813	112120863	E072	10324
chr12	112121888	112121937	E072	11399
chr12	112122047	112122097	E072	11558
chr12	112122118	112122168	E072	11629
chr12	112125136	112125350	E072	14647
chr12	112152787	112153106	E072	42298
chr12	112153115	112153510	E072	42626
chr12	112080574	112080753	E073	-29736
chr12	112091561	112091601	E073	-18888
chr12	112091859	112091917	E073	-18572
chr12	112091934	112092039	E073	-18450
chr12	112102495	112102555	E073	-7934
chr12	112102671	112102725	E073	-7764
chr12	112102766	112102816	E073	-7673
chr12	112121888	112121937	E073	11399
chr12	112122047	112122097	E073	11558
chr12	112122118	112122168	E073	11629
chr12	112125136	112125350	E073	14647
chr12	112073331	112075037	E074	-35452
chr12	112076799	112076922	E074	-33567
chr12	112080293	112080437	E074	-30052
chr12	112080574	112080753	E074	-29736
chr12	112080875	112082060	E074	-28429
chr12	112082158	112082202	E074	-28287
chr12	112091561	112091601	E074	-18888
chr12	112091859	112091917	E074	-18572
chr12	112091934	112092039	E074	-18450
chr12	112093805	112093855	E074	-16634
chr12	112093900	112094228	E074	-16261
chr12	112102766	112102816	E074	-7673
chr12	112121582	112121632	E074	11093
chr12	112121724	112121796	E074	11235
chr12	112121888	112121937	E074	11399
chr12	112125136	112125350	E074	14647
chr12	112073331	112075037	E081	-35452
chr12	112075134	112075332	E081	-35157
chr12	112075381	112075450	E081	-35039
chr12	112076799	112076922	E081	-33567
chr12	112078196	112078770	E081	-31719
chr12	112093805	112093855	E081	-16634
chr12	112093900	112094228	E081	-16261
chr12	112122047	112122097	E081	11558
chr12	112122118	112122168	E081	11629
chr12	112153115	112153510	E081	42626
chr12	112073331	112075037	E082	-35452
chr12	112076799	112076922	E082	-33567
chr12	112078196	112078770	E082	-31719
chr12	112120813	112120863	E082	10324
chr12	112121005	112121049	E082	10516
chr12	112121293	112121343	E082	10804
chr12	112121582	112121632	E082	11093
chr12	112121724	112121796	E082	11235
chr12	112121888	112121937	E082	11399
chr12	112122047	112122097	E082	11558
chr12	112122118	112122168	E082	11629
chr12	112152787	112153106	E082	42298
chr12	112153115	112153510	E082	42626

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr12	112122735	112124415	E067	12246
chr12	112122735	112124415	E068	12246
chr12	112122735	112124415	E069	12246
chr12	112122735	112124415	E070	12246
chr12	112122735	112124415	E071	12246
chr12	112122735	112124415	E072	12246
chr12	112122735	112124415	E073	12246
chr12	112122735	112124415	E074	12246
chr12	112122735	112124415	E081	12246
chr12	112122735	112124415	E082	12246