rs6794945

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

SRPRB : Intron Variant
LOC105374116 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0264 (7901/29886,GnomAD)
T=0240 (7013/29118,TOPMED)
T=0311 (1557/5008,1000G)
T=0316 (1218/3854,ALSPAC)
T=0317 (1175/3708,TWINSUK)

Position: chr3:133799619 (GRCh38.p7) (3q22.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 4 publication(s)

Genomic View: See rs on genome

Enhancer: 62 Enhancers around

Promoter: 19 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 3	NC_000003.12:g.133799619C>T
GRCh37.p13 chr 3	NC_000003.11:g.133518463C>T

Gene: SRPRB, SRP receptor beta subunit(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SRPRB transcript	NM_021203.3:c.	N/A	Intron Variant

Gene: LOC105374116, uncharacterized LOC105374116(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105374116 transcript variant X1	XR_924512.2:n.	N/A	Intron Variant
LOC105374116 transcript variant X2	XR_924513.2:n.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.931	T=0.069
1000Genomes	American	Sub	694	C=0.600	T=0.400
1000Genomes	East Asian	Sub	1008	C=0.537	T=0.463
1000Genomes	Europe	Sub	1006	C=0.666	T=0.334
1000Genomes	Global	Study-wide	5008	C=0.689	T=0.311
1000Genomes	South Asian	Sub	978	C=0.600	T=0.400
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.684	T=0.316
The Genome Aggregation Database	African	Sub	8706	C=0.883	T=0.117
The Genome Aggregation Database	American	Sub	838	C=0.540	T=0.460
The Genome Aggregation Database	East Asian	Sub	1610	C=0.558	T=0.442
The Genome Aggregation Database	Europe	Sub	18430	C=0.689	T=0.310
The Genome Aggregation Database	Global	Study-wide	29886	C=0.735	T=0.264
The Genome Aggregation Database	Other	Sub	302	C=0.760	T=0.240
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.759	T=0.240
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.683	T=0.317

PMID	Title	Author	Journal
19084217	Variants in TF and HFE explain approximately 40% of genetic variation in serum-transferrin levels.	Benyamin B	Am J Hum Genet
19673882	A novel association between a SNP in CYBRD1 and serum ferritin levels in a cohort study of HFE hereditary haemochromatosis.	Constantine CC	Br J Haematol
21665994	Genome-wide association study identifies two loci strongly affecting transferrin glycosylation.	Kutalik Z	Hum Mol Genet
22761678	Associations between single nucleotide polymorphisms in iron-related genes and iron status in multiethnic populations.	McLaren CE	PLoS One

SNP ID	p-value	Traits	Study
rs6794945	6.06E-13	alcohol consumption	21665994

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
There is no eQTL annotation for this SNP

Probe ID	Position	Gene	beta	p-value
cg16414030	chr3:133502952		-0.126960217493355	5.1608e-48
cg08048268	chr3:133502702		-0.181860177648547	7.3786e-44
cg01448562	chr3:133502909		-0.0799351268299212	2.3946e-43
cg16275903	chr3:133524006	SRPRB	0.0750721079120634	1.6591e-32
cg11941060	chr3:133502564		-0.090781521030358	4.5922e-32
cg08439880	chr3:133502540		-0.0967276104602738	2.3831e-30
cg20276088	chr3:133502917		-0.0478180082747938	2.4907e-29

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	133482923	133483028	E067	-35435
chr3	133483054	133483594	E067	-34869
chr3	133483998	133484070	E067	-34393
chr3	133562885	133562960	E067	44422
chr3	133482562	133482616	E068	-35847
chr3	133482923	133483028	E068	-35435
chr3	133483054	133483594	E068	-34869
chr3	133473014	133473073	E069	-45390
chr3	133473315	133473659	E069	-44804
chr3	133476260	133476458	E069	-42005
chr3	133482562	133482616	E069	-35847
chr3	133482923	133483028	E069	-35435
chr3	133483054	133483594	E069	-34869
chr3	133483998	133484070	E069	-34393
chr3	133484337	133484387	E069	-34076
chr3	133540603	133541021	E069	22140
chr3	133541191	133541245	E069	22728
chr3	133482923	133483028	E070	-35435
chr3	133483054	133483594	E070	-34869
chr3	133547093	133547193	E070	28630
chr3	133547516	133547745	E070	29053
chr3	133547924	133548172	E070	29461
chr3	133473014	133473073	E071	-45390
chr3	133473315	133473659	E071	-44804
chr3	133482562	133482616	E071	-35847
chr3	133482923	133483028	E071	-35435
chr3	133483054	133483594	E071	-34869
chr3	133483998	133484070	E071	-34393
chr3	133484337	133484387	E071	-34076
chr3	133540337	133540417	E071	21874
chr3	133473014	133473073	E072	-45390
chr3	133482923	133483028	E072	-35435
chr3	133483054	133483594	E072	-34869
chr3	133483998	133484070	E072	-34393
chr3	133484337	133484387	E072	-34076
chr3	133482923	133483028	E073	-35435
chr3	133483054	133483594	E073	-34869
chr3	133540006	133540074	E073	21543
chr3	133540337	133540417	E073	21874
chr3	133540603	133541021	E073	22140
chr3	133541035	133541081	E073	22572
chr3	133541191	133541245	E073	22728
chr3	133473014	133473073	E074	-45390
chr3	133473315	133473659	E074	-44804
chr3	133476260	133476458	E074	-42005
chr3	133482562	133482616	E074	-35847
chr3	133482923	133483028	E074	-35435
chr3	133483054	133483594	E074	-34869
chr3	133483998	133484070	E074	-34393
chr3	133484337	133484387	E074	-34076
chr3	133540006	133540074	E074	21543
chr3	133540337	133540417	E074	21874
chr3	133540603	133541021	E074	22140
chr3	133541035	133541081	E074	22572
chr3	133541191	133541245	E074	22728
chr3	133541431	133541497	E074	22968
chr3	133541623	133541762	E074	23160
chr3	133541910	133541964	E074	23447
chr3	133526132	133526214	E081	7669
chr3	133547516	133547745	E082	29053
chr3	133547924	133548172	E082	29461
chr3	133548284	133548391	E082	29821

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr3	133524082	133525550	E067	5619
chr3	133525588	133525634	E067	7125
chr3	133524082	133525550	E068	5619
chr3	133525588	133525634	E068	7125
chr3	133524082	133525550	E069	5619
chr3	133524082	133525550	E070	5619
chr3	133525588	133525634	E070	7125
chr3	133524082	133525550	E071	5619
chr3	133525588	133525634	E071	7125
chr3	133524082	133525550	E072	5619
chr3	133525588	133525634	E072	7125
chr3	133524082	133525550	E073	5619
chr3	133525588	133525634	E073	7125
chr3	133524082	133525550	E074	5619
chr3	133525588	133525634	E074	7125
chr3	133524082	133525550	E081	5619
chr3	133525588	133525634	E081	7125
chr3	133524082	133525550	E082	5619
chr3	133525588	133525634	E082	7125

rs6794945

Genomic Coordinates

Gene: SRPRB, SRP receptor beta subunit(plus strand)

Gene: LOC105374116, uncharacterized LOC105374116(minus strand)

Population Frequency

P-Value

eQTL of rs6794945 in Brain tissues (GTEx Analysis Release V7)

meQTL of rs6794945 in Fetal Brain

Genomic View

Chromatin Interaction

Enhancer Annotation (GRCh37.p13)

Promoter Annotation (GRCh37.p13)