rs4854761

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

None

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0325 (9724/29924,GnomAD)
A=0333 (9707/29118,TOPMED)
A=0358 (1792/5008,1000G)
A=0331 (1277/3854,ALSPAC)
A=0334 (1237/3708,TWINSUK)

Position: chr3:133779945 (GRCh38.p7) (3q22.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 2 publication(s)

Genomic View: See rs on genome

Enhancer: 83 Enhancers around

Promoter: 51 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 3	NC_000003.12:g.133779945G>A
GRCh37.p13 chr 3	NC_000003.11:g.133498789G>A
TF RefSeqGene	NG_013080.1:g.38813G>A

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.741	A=0.259
1000Genomes	American	Sub	694	G=0.600	A=0.400
1000Genomes	East Asian	Sub	1008	G=0.578	A=0.422
1000Genomes	Europe	Sub	1006	G=0.654	A=0.346
1000Genomes	Global	Study-wide	5008	G=0.642	A=0.358
1000Genomes	South Asian	Sub	978	G=0.600	A=0.400
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.669	A=0.331
The Genome Aggregation Database	African	Sub	8706	G=0.703	A=0.297
The Genome Aggregation Database	American	Sub	836	G=0.540	A=0.460
The Genome Aggregation Database	East Asian	Sub	1606	G=0.601	A=0.399
The Genome Aggregation Database	Europe	Sub	18474	G=0.673	A=0.326
The Genome Aggregation Database	Global	Study-wide	29924	G=0.675	A=0.325
The Genome Aggregation Database	Other	Sub	302	G=0.760	A=0.240
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.666	A=0.333
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.666	A=0.334

PMID	Title	Author	Journal
23092954	SHAVE: shrinkage estimator measured for multiple visits increases power in GWAS of quantitative traits.	Meirelles OD	Eur J Hum Genet
21665994	Genome-wide association study identifies two loci strongly affecting transferrin glycosylation.	Kutalik Z	Hum Mol Genet

P-Value

SNP ID	p-value	Traits	Study
rs4854761	2E-12	alcohol consumption	21665994

eQTL of rs4854761 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 rs4854761 in Fetal Brain

Probe ID	Position	Gene	beta	p-value
cg08048268	chr3:133502702		-0.155654296602091	4.4964e-32
cg16414030	chr3:133502952		-0.103714415743927	6.1723e-30
cg01448562	chr3:133502909		-0.0665904759147823	2.4341e-29
cg16275903	chr3:133524006	SRPRB	0.062785081445199	1.9005e-23
cg11941060	chr3:133502564		-0.0721517288598247	2.1283e-20
cg08439880	chr3:133502540		-0.0778624073043589	4.0865e-20
cg20276088	chr3:133502917		-0.0380648386319362	4.8919e-19

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	133461397	133461916	E067	-36873
chr3	133461945	133462055	E067	-36734
chr3	133464069	133464119	E067	-34670
chr3	133464448	133464526	E067	-34263
chr3	133482923	133483028	E067	-15761
chr3	133483054	133483594	E067	-15195
chr3	133483998	133484070	E067	-14719
chr3	133464069	133464119	E068	-34670
chr3	133482562	133482616	E068	-16173
chr3	133482923	133483028	E068	-15761
chr3	133483054	133483594	E068	-15195
chr3	133461397	133461916	E069	-36873
chr3	133461945	133462055	E069	-36734
chr3	133464069	133464119	E069	-34670
chr3	133473014	133473073	E069	-25716
chr3	133473315	133473659	E069	-25130
chr3	133476260	133476458	E069	-22331
chr3	133482562	133482616	E069	-16173
chr3	133482923	133483028	E069	-15761
chr3	133483054	133483594	E069	-15195
chr3	133483998	133484070	E069	-14719
chr3	133484337	133484387	E069	-14402
chr3	133540603	133541021	E069	41814
chr3	133541191	133541245	E069	42402
chr3	133482923	133483028	E070	-15761
chr3	133483054	133483594	E070	-15195
chr3	133547093	133547193	E070	48304
chr3	133547516	133547745	E070	48727
chr3	133547924	133548172	E070	49135
chr3	133461397	133461916	E071	-36873
chr3	133461945	133462055	E071	-36734
chr3	133464069	133464119	E071	-34670
chr3	133473014	133473073	E071	-25716
chr3	133473315	133473659	E071	-25130
chr3	133482562	133482616	E071	-16173
chr3	133482923	133483028	E071	-15761
chr3	133483054	133483594	E071	-15195
chr3	133483998	133484070	E071	-14719
chr3	133484337	133484387	E071	-14402
chr3	133540337	133540417	E071	41548
chr3	133461397	133461916	E072	-36873
chr3	133461945	133462055	E072	-36734
chr3	133464069	133464119	E072	-34670
chr3	133464448	133464526	E072	-34263
chr3	133473014	133473073	E072	-25716
chr3	133482923	133483028	E072	-15761
chr3	133483054	133483594	E072	-15195
chr3	133483998	133484070	E072	-14719
chr3	133484337	133484387	E072	-14402
chr3	133461397	133461916	E073	-36873
chr3	133461945	133462055	E073	-36734
chr3	133464448	133464526	E073	-34263
chr3	133482923	133483028	E073	-15761
chr3	133483054	133483594	E073	-15195
chr3	133540006	133540074	E073	41217
chr3	133540337	133540417	E073	41548
chr3	133540603	133541021	E073	41814
chr3	133541035	133541081	E073	42246
chr3	133541191	133541245	E073	42402
chr3	133461397	133461916	E074	-36873
chr3	133461945	133462055	E074	-36734
chr3	133464069	133464119	E074	-34670
chr3	133473014	133473073	E074	-25716
chr3	133473315	133473659	E074	-25130
chr3	133476260	133476458	E074	-22331
chr3	133482562	133482616	E074	-16173
chr3	133482923	133483028	E074	-15761
chr3	133483054	133483594	E074	-15195
chr3	133483998	133484070	E074	-14719
chr3	133484337	133484387	E074	-14402
chr3	133540006	133540074	E074	41217
chr3	133540337	133540417	E074	41548
chr3	133540603	133541021	E074	41814
chr3	133541035	133541081	E074	42246
chr3	133541191	133541245	E074	42402
chr3	133541431	133541497	E074	42642
chr3	133541623	133541762	E074	42834
chr3	133541910	133541964	E074	43121
chr3	133526132	133526214	E081	27343
chr3	133464448	133464526	E082	-34263
chr3	133547516	133547745	E082	48727
chr3	133547924	133548172	E082	49135
chr3	133548284	133548391	E082	49495

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr3	133464975	133465152	E067	-33637
chr3	133465195	133465439	E067	-33350
chr3	133465691	133465761	E067	-33028
chr3	133468272	133468322	E067	-30467
chr3	133524082	133525550	E067	25293
chr3	133525588	133525634	E067	26799
chr3	133464975	133465152	E068	-33637
chr3	133465195	133465439	E068	-33350
chr3	133465691	133465761	E068	-33028
chr3	133468272	133468322	E068	-30467
chr3	133524082	133525550	E068	25293
chr3	133525588	133525634	E068	26799
chr3	133464975	133465152	E069	-33637
chr3	133465195	133465439	E069	-33350
chr3	133465691	133465761	E069	-33028
chr3	133468272	133468322	E069	-30467
chr3	133524082	133525550	E069	25293
chr3	133465195	133465439	E070	-33350
chr3	133524082	133525550	E070	25293
chr3	133525588	133525634	E070	26799
chr3	133464975	133465152	E071	-33637
chr3	133465195	133465439	E071	-33350
chr3	133465691	133465761	E071	-33028
chr3	133468272	133468322	E071	-30467
chr3	133524082	133525550	E071	25293
chr3	133525588	133525634	E071	26799
chr3	133464975	133465152	E072	-33637
chr3	133465195	133465439	E072	-33350
chr3	133465691	133465761	E072	-33028
chr3	133468272	133468322	E072	-30467
chr3	133524082	133525550	E072	25293
chr3	133525588	133525634	E072	26799
chr3	133464975	133465152	E073	-33637
chr3	133465195	133465439	E073	-33350
chr3	133465691	133465761	E073	-33028
chr3	133468272	133468322	E073	-30467
chr3	133524082	133525550	E073	25293
chr3	133525588	133525634	E073	26799
chr3	133464975	133465152	E074	-33637
chr3	133465195	133465439	E074	-33350
chr3	133465691	133465761	E074	-33028
chr3	133468272	133468322	E074	-30467
chr3	133524082	133525550	E074	25293
chr3	133525588	133525634	E074	26799
chr3	133464975	133465152	E081	-33637
chr3	133524082	133525550	E081	25293
chr3	133525588	133525634	E081	26799
chr3	133464975	133465152	E082	-33637
chr3	133465195	133465439	E082	-33350
chr3	133524082	133525550	E082	25293
chr3	133525588	133525634	E082	26799