rs1525889

Organism: Homo sapiens

Alleles: A>C

Gene : Feature

TF : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C=0294 (8821/29952,GnomAD)
C=0282 (8222/29118,TOPMED)
C=0328 (1643/5008,1000G)
C=0333 (1284/3854,ALSPAC)
C=0336 (1246/3708,TWINSUK)

Position: chr3:133771189 (GRCh38.p7) (3q22.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 2 publication(s)

Genomic View: See rs on genome

Enhancer: 61 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.133771189A>C
GRCh37.p13 chr 3	NC_000003.11:g.133490033A>C
TF RefSeqGene	NG_013080.1:g.30057A>C

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	A=0.856	C=0.144
1000Genomes	American	Sub	694	A=0.610	C=0.390
1000Genomes	East Asian	Sub	1008	A=0.576	C=0.424
1000Genomes	Europe	Sub	1006	A=0.653	C=0.347
1000Genomes	Global	Study-wide	5008	A=0.672	C=0.328
1000Genomes	South Asian	Sub	978	A=0.590	C=0.410
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.667	C=0.333
The Genome Aggregation Database	African	Sub	8720	A=0.811	C=0.189
The Genome Aggregation Database	American	Sub	836	A=0.540	C=0.460
The Genome Aggregation Database	East Asian	Sub	1612	A=0.604	C=0.396
The Genome Aggregation Database	Europe	Sub	18482	A=0.671	C=0.328
The Genome Aggregation Database	Global	Study-wide	29952	A=0.705	C=0.294
The Genome Aggregation Database	Other	Sub	302	A=0.740	C=0.260
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.717	C=0.282
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.664	C=0.336

PMID	Title	Author	Journal
26582562	Signatures of Evolutionary Adaptation in Quantitative Trait Loci Influencing Trace Element Homeostasis in Liver.	Engelken J	Mol Biol Evol
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
rs1525889	8.21E-13	alcohol consumption	21665994

eQTL of rs1525889 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 rs1525889 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	-28117
chr3	133461945	133462055	E067	-27978
chr3	133464069	133464119	E067	-25914
chr3	133464448	133464526	E067	-25507
chr3	133482923	133483028	E067	-7005
chr3	133483054	133483594	E067	-6439
chr3	133483998	133484070	E067	-5963
chr3	133464069	133464119	E068	-25914
chr3	133482562	133482616	E068	-7417
chr3	133482923	133483028	E068	-7005
chr3	133483054	133483594	E068	-6439
chr3	133461397	133461916	E069	-28117
chr3	133461945	133462055	E069	-27978
chr3	133464069	133464119	E069	-25914
chr3	133473014	133473073	E069	-16960
chr3	133473315	133473659	E069	-16374
chr3	133476260	133476458	E069	-13575
chr3	133482562	133482616	E069	-7417
chr3	133482923	133483028	E069	-7005
chr3	133483054	133483594	E069	-6439
chr3	133483998	133484070	E069	-5963
chr3	133484337	133484387	E069	-5646
chr3	133482923	133483028	E070	-7005
chr3	133483054	133483594	E070	-6439
chr3	133461397	133461916	E071	-28117
chr3	133461945	133462055	E071	-27978
chr3	133464069	133464119	E071	-25914
chr3	133473014	133473073	E071	-16960
chr3	133473315	133473659	E071	-16374
chr3	133482562	133482616	E071	-7417
chr3	133482923	133483028	E071	-7005
chr3	133483054	133483594	E071	-6439
chr3	133483998	133484070	E071	-5963
chr3	133484337	133484387	E071	-5646
chr3	133461397	133461916	E072	-28117
chr3	133461945	133462055	E072	-27978
chr3	133464069	133464119	E072	-25914
chr3	133464448	133464526	E072	-25507
chr3	133473014	133473073	E072	-16960
chr3	133482923	133483028	E072	-7005
chr3	133483054	133483594	E072	-6439
chr3	133483998	133484070	E072	-5963
chr3	133484337	133484387	E072	-5646
chr3	133461397	133461916	E073	-28117
chr3	133461945	133462055	E073	-27978
chr3	133464448	133464526	E073	-25507
chr3	133482923	133483028	E073	-7005
chr3	133483054	133483594	E073	-6439
chr3	133461397	133461916	E074	-28117
chr3	133461945	133462055	E074	-27978
chr3	133464069	133464119	E074	-25914
chr3	133473014	133473073	E074	-16960
chr3	133473315	133473659	E074	-16374
chr3	133476260	133476458	E074	-13575
chr3	133482562	133482616	E074	-7417
chr3	133482923	133483028	E074	-7005
chr3	133483054	133483594	E074	-6439
chr3	133483998	133484070	E074	-5963
chr3	133484337	133484387	E074	-5646
chr3	133526132	133526214	E081	36099
chr3	133464448	133464526	E082	-25507

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr3	133464975	133465152	E067	-24881
chr3	133465195	133465439	E067	-24594
chr3	133465691	133465761	E067	-24272
chr3	133468272	133468322	E067	-21711
chr3	133524082	133525550	E067	34049
chr3	133525588	133525634	E067	35555
chr3	133464975	133465152	E068	-24881
chr3	133465195	133465439	E068	-24594
chr3	133465691	133465761	E068	-24272
chr3	133468272	133468322	E068	-21711
chr3	133524082	133525550	E068	34049
chr3	133525588	133525634	E068	35555
chr3	133464975	133465152	E069	-24881
chr3	133465195	133465439	E069	-24594
chr3	133465691	133465761	E069	-24272
chr3	133468272	133468322	E069	-21711
chr3	133524082	133525550	E069	34049
chr3	133465195	133465439	E070	-24594
chr3	133524082	133525550	E070	34049
chr3	133525588	133525634	E070	35555
chr3	133464975	133465152	E071	-24881
chr3	133465195	133465439	E071	-24594
chr3	133465691	133465761	E071	-24272
chr3	133468272	133468322	E071	-21711
chr3	133524082	133525550	E071	34049
chr3	133525588	133525634	E071	35555
chr3	133464975	133465152	E072	-24881
chr3	133465195	133465439	E072	-24594
chr3	133465691	133465761	E072	-24272
chr3	133468272	133468322	E072	-21711
chr3	133524082	133525550	E072	34049
chr3	133525588	133525634	E072	35555
chr3	133464975	133465152	E073	-24881
chr3	133465195	133465439	E073	-24594
chr3	133465691	133465761	E073	-24272
chr3	133468272	133468322	E073	-21711
chr3	133524082	133525550	E073	34049
chr3	133525588	133525634	E073	35555
chr3	133464975	133465152	E074	-24881
chr3	133465195	133465439	E074	-24594
chr3	133465691	133465761	E074	-24272
chr3	133468272	133468322	E074	-21711
chr3	133524082	133525550	E074	34049
chr3	133525588	133525634	E074	35555
chr3	133464975	133465152	E081	-24881
chr3	133524082	133525550	E081	34049
chr3	133525588	133525634	E081	35555
chr3	133464975	133465152	E082	-24881
chr3	133465195	133465439	E082	-24594
chr3	133524082	133525550	E082	34049
chr3	133525588	133525634	E082	35555