rs8177240

Organism: Homo sapiens

Alleles: T>C / T>G

Gene : Feature

TF : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0293 (8773/29886,GnomAD)
G=0274 (7985/29118,TOPMED)
G=0325 (1630/5008,1000G)
G=0340 (1311/3854,ALSPAC)
G=0340 (1261/3708,TWINSUK)

Position: chr3:133758857 (GRCh38.p7) (3q22.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 4 publication(s)

Genomic View: See rs on genome

Enhancer: 67 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.133758857T>C
GRCh38.p7 chr 3	NC_000003.12:g.133758857T>G
GRCh37.p13 chr 3	NC_000003.11:g.133477701T>C
GRCh37.p13 chr 3	NC_000003.11:g.133477701T>G
TF RefSeqGene	NG_013080.1:g.17725T>C
TF RefSeqGene	NG_013080.1:g.17725T>G

Gene: TF, transferrin(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
TF transcript variant 1	NM_001063.3:c.	N/A	Intron Variant
TF transcript variant X1	XM_017007089.1:c.	N/A	Intron Variant
TF transcript variant X2	XM_017007090.1:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.879	G=0.121
1000Genomes	American	Sub	694	T=0.610	G=0.390
1000Genomes	East Asian	Sub	1008	T=0.567	G=0.433
1000Genomes	Europe	Sub	1006	T=0.650	G=0.350
1000Genomes	Global	Study-wide	5008	T=0.675	G=0.325
1000Genomes	South Asian	Sub	978	T=0.580	G=0.420
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.660	G=0.340
The Genome Aggregation Database	African	Sub	8688	T=0.827	G=0.173
The Genome Aggregation Database	American	Sub	834	T=0.540	G=0.460
The Genome Aggregation Database	East Asian	Sub	1614	T=0.600	G=0.400
The Genome Aggregation Database	Europe	Sub	18450	T=0.666	G=0.333
The Genome Aggregation Database	Global	Study-wide	29886	T=0.706	G=0.293
The Genome Aggregation Database	Other	Sub	300	T=0.730	G=0.270
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.725	G=0.274
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.660	G=0.340

PMID	Title	Author	Journal
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
26159428	Iron and hepcidin as risk factors in atherosclerosis: what do the genes say?	Galesloot TE	BMC Genet
21483845	Genome-wide association study identifies genetic loci associated with iron deficiency.	McLaren CE	PLoS One

P-Value

SNP ID	p-value	Traits	Study
rs8177240	3.12E-13	alcohol consumption	21665994

eQTL of rs8177240 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 rs8177240 in Fetal Brain

Probe ID	Position	Gene	beta	p-value
cg08048268	chr3:133502702		-0.17017511422821	2.3599e-39
cg16414030	chr3:133502952		-0.11466174595369	9.0636e-38
cg01448562	chr3:133502909		-0.0732129620427509	3.0343e-36
cg16275903	chr3:133524006	SRPRB	0.0685847121065922	9.4108e-28
cg11941060	chr3:133502564		-0.0788008210182232	6.9791e-24
cg08439880	chr3:133502540		-0.0851592321203418	1.2892e-23
cg20276088	chr3:133502917		-0.0423413690281787	2.9867e-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	133436424	133436504	E067	-46366
chr3	133461397	133461916	E067	-20954
chr3	133461945	133462055	E067	-20815
chr3	133464069	133464119	E067	-18751
chr3	133464448	133464526	E067	-18344
chr3	133482923	133483028	E067	53
chr3	133483054	133483594	E067	184
chr3	133483998	133484070	E067	1128
chr3	133436424	133436504	E068	-46366
chr3	133464069	133464119	E068	-18751
chr3	133482562	133482616	E068	-254
chr3	133482923	133483028	E068	53
chr3	133483054	133483594	E068	184
chr3	133436424	133436504	E069	-46366
chr3	133461397	133461916	E069	-20954
chr3	133461945	133462055	E069	-20815
chr3	133464069	133464119	E069	-18751
chr3	133473014	133473073	E069	-9797
chr3	133473315	133473659	E069	-9211
chr3	133476260	133476458	E069	-6412
chr3	133482562	133482616	E069	-254
chr3	133482923	133483028	E069	53
chr3	133483054	133483594	E069	184
chr3	133483998	133484070	E069	1128
chr3	133484337	133484387	E069	1467
chr3	133482923	133483028	E070	53
chr3	133483054	133483594	E070	184
chr3	133436424	133436504	E071	-46366
chr3	133461397	133461916	E071	-20954
chr3	133461945	133462055	E071	-20815
chr3	133464069	133464119	E071	-18751
chr3	133473014	133473073	E071	-9797
chr3	133473315	133473659	E071	-9211
chr3	133482562	133482616	E071	-254
chr3	133482923	133483028	E071	53
chr3	133483054	133483594	E071	184
chr3	133483998	133484070	E071	1128
chr3	133484337	133484387	E071	1467
chr3	133461397	133461916	E072	-20954
chr3	133461945	133462055	E072	-20815
chr3	133464069	133464119	E072	-18751
chr3	133464448	133464526	E072	-18344
chr3	133473014	133473073	E072	-9797
chr3	133482923	133483028	E072	53
chr3	133483054	133483594	E072	184
chr3	133483998	133484070	E072	1128
chr3	133484337	133484387	E072	1467
chr3	133436424	133436504	E073	-46366
chr3	133461397	133461916	E073	-20954
chr3	133461945	133462055	E073	-20815
chr3	133464448	133464526	E073	-18344
chr3	133482923	133483028	E073	53
chr3	133483054	133483594	E073	184
chr3	133436424	133436504	E074	-46366
chr3	133461397	133461916	E074	-20954
chr3	133461945	133462055	E074	-20815
chr3	133464069	133464119	E074	-18751
chr3	133473014	133473073	E074	-9797
chr3	133473315	133473659	E074	-9211
chr3	133476260	133476458	E074	-6412
chr3	133482562	133482616	E074	-254
chr3	133482923	133483028	E074	53
chr3	133483054	133483594	E074	184
chr3	133483998	133484070	E074	1128
chr3	133484337	133484387	E074	1467
chr3	133526132	133526214	E081	43262
chr3	133464448	133464526	E082	-18344

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr3	133464975	133465152	E067	-17718
chr3	133465195	133465439	E067	-17431
chr3	133465691	133465761	E067	-17109
chr3	133468272	133468322	E067	-14548
chr3	133524082	133525550	E067	41212
chr3	133525588	133525634	E067	42718
chr3	133464975	133465152	E068	-17718
chr3	133465195	133465439	E068	-17431
chr3	133465691	133465761	E068	-17109
chr3	133468272	133468322	E068	-14548
chr3	133524082	133525550	E068	41212
chr3	133525588	133525634	E068	42718
chr3	133464975	133465152	E069	-17718
chr3	133465195	133465439	E069	-17431
chr3	133465691	133465761	E069	-17109
chr3	133468272	133468322	E069	-14548
chr3	133524082	133525550	E069	41212
chr3	133465195	133465439	E070	-17431
chr3	133524082	133525550	E070	41212
chr3	133525588	133525634	E070	42718
chr3	133464975	133465152	E071	-17718
chr3	133465195	133465439	E071	-17431
chr3	133465691	133465761	E071	-17109
chr3	133468272	133468322	E071	-14548
chr3	133524082	133525550	E071	41212
chr3	133525588	133525634	E071	42718
chr3	133464975	133465152	E072	-17718
chr3	133465195	133465439	E072	-17431
chr3	133465691	133465761	E072	-17109
chr3	133468272	133468322	E072	-14548
chr3	133524082	133525550	E072	41212
chr3	133525588	133525634	E072	42718
chr3	133464975	133465152	E073	-17718
chr3	133465195	133465439	E073	-17431
chr3	133465691	133465761	E073	-17109
chr3	133468272	133468322	E073	-14548
chr3	133524082	133525550	E073	41212
chr3	133525588	133525634	E073	42718
chr3	133464975	133465152	E074	-17718
chr3	133465195	133465439	E074	-17431
chr3	133465691	133465761	E074	-17109
chr3	133468272	133468322	E074	-14548
chr3	133524082	133525550	E074	41212
chr3	133525588	133525634	E074	42718
chr3	133464975	133465152	E081	-17718
chr3	133524082	133525550	E081	41212
chr3	133525588	133525634	E081	42718
chr3	133464975	133465152	E082	-17718
chr3	133465195	133465439	E082	-17431
chr3	133524082	133525550	E082	41212
chr3	133525588	133525634	E082	42718