rs4854762

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

None

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0312 (9341/29890,GnomAD)
A=0311 (9055/29118,TOPMED)
A=0352 (1762/5008,1000G)
A=0332 (1281/3854,ALSPAC)
A=0334 (1240/3708,TWINSUK)

Position: chr3:133780219 (GRCh38.p7) (3q22.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 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.133780219G>A
GRCh37.p13 chr 3	NC_000003.11:g.133499063G>A
TF RefSeqGene	NG_013080.1:g.39087G>A

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.768	A=0.232
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=0.648	A=0.352
1000Genomes	South Asian	Sub	978	G=0.590	A=0.410
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.668	A=0.332
The Genome Aggregation Database	African	Sub	8690	G=0.746	A=0.254
The Genome Aggregation Database	American	Sub	832	G=0.540	A=0.460
The Genome Aggregation Database	East Asian	Sub	1612	G=0.602	A=0.398
The Genome Aggregation Database	Europe	Sub	18454	G=0.673	A=0.326
The Genome Aggregation Database	Global	Study-wide	29890	G=0.687	A=0.312
The Genome Aggregation Database	Other	Sub	302	G=0.760	A=0.240
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.689	A=0.311
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.666	A=0.334

PMID	Title	Author	Journal
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
rs4854762	1.07E-13	alcohol consumption	21665994

eQTL of rs4854762 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 rs4854762 in Fetal Brain

Probe ID	Position	Gene	beta	p-value
cg08048268	chr3:133502702		-0.168130975169641	2.2918e-38
cg16414030	chr3:133502952		-0.112432326932529	5.9804e-36
cg01448562	chr3:133502909		-0.0724171823735374	1.6299e-35
cg16275903	chr3:133524006	SRPRB	0.0674502400334624	7.6792e-27
cg08439880	chr3:133502540		-0.0848206966307129	1.1749e-23
cg11941060	chr3:133502564		-0.0775058022947404	3.7183e-23
cg20276088	chr3:133502917		-0.0418805416525961	7.0551e-23

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	-37147
chr3	133461945	133462055	E067	-37008
chr3	133464069	133464119	E067	-34944
chr3	133464448	133464526	E067	-34537
chr3	133482923	133483028	E067	-16035
chr3	133483054	133483594	E067	-15469
chr3	133483998	133484070	E067	-14993
chr3	133464069	133464119	E068	-34944
chr3	133482562	133482616	E068	-16447
chr3	133482923	133483028	E068	-16035
chr3	133483054	133483594	E068	-15469
chr3	133461397	133461916	E069	-37147
chr3	133461945	133462055	E069	-37008
chr3	133464069	133464119	E069	-34944
chr3	133473014	133473073	E069	-25990
chr3	133473315	133473659	E069	-25404
chr3	133476260	133476458	E069	-22605
chr3	133482562	133482616	E069	-16447
chr3	133482923	133483028	E069	-16035
chr3	133483054	133483594	E069	-15469
chr3	133483998	133484070	E069	-14993
chr3	133484337	133484387	E069	-14676
chr3	133540603	133541021	E069	41540
chr3	133541191	133541245	E069	42128
chr3	133482923	133483028	E070	-16035
chr3	133483054	133483594	E070	-15469
chr3	133547093	133547193	E070	48030
chr3	133547516	133547745	E070	48453
chr3	133547924	133548172	E070	48861
chr3	133461397	133461916	E071	-37147
chr3	133461945	133462055	E071	-37008
chr3	133464069	133464119	E071	-34944
chr3	133473014	133473073	E071	-25990
chr3	133473315	133473659	E071	-25404
chr3	133482562	133482616	E071	-16447
chr3	133482923	133483028	E071	-16035
chr3	133483054	133483594	E071	-15469
chr3	133483998	133484070	E071	-14993
chr3	133484337	133484387	E071	-14676
chr3	133540337	133540417	E071	41274
chr3	133461397	133461916	E072	-37147
chr3	133461945	133462055	E072	-37008
chr3	133464069	133464119	E072	-34944
chr3	133464448	133464526	E072	-34537
chr3	133473014	133473073	E072	-25990
chr3	133482923	133483028	E072	-16035
chr3	133483054	133483594	E072	-15469
chr3	133483998	133484070	E072	-14993
chr3	133484337	133484387	E072	-14676
chr3	133461397	133461916	E073	-37147
chr3	133461945	133462055	E073	-37008
chr3	133464448	133464526	E073	-34537
chr3	133482923	133483028	E073	-16035
chr3	133483054	133483594	E073	-15469
chr3	133540006	133540074	E073	40943
chr3	133540337	133540417	E073	41274
chr3	133540603	133541021	E073	41540
chr3	133541035	133541081	E073	41972
chr3	133541191	133541245	E073	42128
chr3	133461397	133461916	E074	-37147
chr3	133461945	133462055	E074	-37008
chr3	133464069	133464119	E074	-34944
chr3	133473014	133473073	E074	-25990
chr3	133473315	133473659	E074	-25404
chr3	133476260	133476458	E074	-22605
chr3	133482562	133482616	E074	-16447
chr3	133482923	133483028	E074	-16035
chr3	133483054	133483594	E074	-15469
chr3	133483998	133484070	E074	-14993
chr3	133484337	133484387	E074	-14676
chr3	133540006	133540074	E074	40943
chr3	133540337	133540417	E074	41274
chr3	133540603	133541021	E074	41540
chr3	133541035	133541081	E074	41972
chr3	133541191	133541245	E074	42128
chr3	133541431	133541497	E074	42368
chr3	133541623	133541762	E074	42560
chr3	133541910	133541964	E074	42847
chr3	133526132	133526214	E081	27069
chr3	133464448	133464526	E082	-34537
chr3	133547516	133547745	E082	48453
chr3	133547924	133548172	E082	48861
chr3	133548284	133548391	E082	49221

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr3	133464975	133465152	E067	-33911
chr3	133465195	133465439	E067	-33624
chr3	133465691	133465761	E067	-33302
chr3	133468272	133468322	E067	-30741
chr3	133524082	133525550	E067	25019
chr3	133525588	133525634	E067	26525
chr3	133464975	133465152	E068	-33911
chr3	133465195	133465439	E068	-33624
chr3	133465691	133465761	E068	-33302
chr3	133468272	133468322	E068	-30741
chr3	133524082	133525550	E068	25019
chr3	133525588	133525634	E068	26525
chr3	133464975	133465152	E069	-33911
chr3	133465195	133465439	E069	-33624
chr3	133465691	133465761	E069	-33302
chr3	133468272	133468322	E069	-30741
chr3	133524082	133525550	E069	25019
chr3	133465195	133465439	E070	-33624
chr3	133524082	133525550	E070	25019
chr3	133525588	133525634	E070	26525
chr3	133464975	133465152	E071	-33911
chr3	133465195	133465439	E071	-33624
chr3	133465691	133465761	E071	-33302
chr3	133468272	133468322	E071	-30741
chr3	133524082	133525550	E071	25019
chr3	133525588	133525634	E071	26525
chr3	133464975	133465152	E072	-33911
chr3	133465195	133465439	E072	-33624
chr3	133465691	133465761	E072	-33302
chr3	133468272	133468322	E072	-30741
chr3	133524082	133525550	E072	25019
chr3	133525588	133525634	E072	26525
chr3	133464975	133465152	E073	-33911
chr3	133465195	133465439	E073	-33624
chr3	133465691	133465761	E073	-33302
chr3	133468272	133468322	E073	-30741
chr3	133524082	133525550	E073	25019
chr3	133525588	133525634	E073	26525
chr3	133464975	133465152	E074	-33911
chr3	133465195	133465439	E074	-33624
chr3	133465691	133465761	E074	-33302
chr3	133468272	133468322	E074	-30741
chr3	133524082	133525550	E074	25019
chr3	133525588	133525634	E074	26525
chr3	133464975	133465152	E081	-33911
chr3	133524082	133525550	E081	25019
chr3	133525588	133525634	E081	26525
chr3	133464975	133465152	E082	-33911
chr3	133465195	133465439	E082	-33624
chr3	133524082	133525550	E082	25019
chr3	133525588	133525634	E082	26525