rs1553009

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

None

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0150 (4500/29960,GnomAD)
A=0147 (4292/29118,TOPMED)
A=0149 (746/5008,1000G)
A=0201 (773/3854,ALSPAC)
A=0207 (766/3708,TWINSUK)

Position: chr7:45869395 (GRCh38.p7) (7p12.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 9 publication(s)

Genomic View: See rs on genome

Enhancer: 1 Enhancer around

Promoter: 6 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 7	NC_000007.14:g.45869395G>A
GRCh37.p13 chr 7	NC_000007.13:g.45908994G>A

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.943	A=0.057
1000Genomes	American	Sub	694	G=0.800	A=0.200
1000Genomes	East Asian	Sub	1008	G=0.746	A=0.254
1000Genomes	Europe	Sub	1006	G=0.816	A=0.184
1000Genomes	Global	Study-wide	5008	G=0.851	A=0.149
1000Genomes	South Asian	Sub	978	G=0.910	A=0.090
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.799	A=0.201
The Genome Aggregation Database	African	Sub	8722	G=0.916	A=0.084
The Genome Aggregation Database	American	Sub	836	G=0.810	A=0.190
The Genome Aggregation Database	East Asian	Sub	1614	G=0.719	A=0.281
The Genome Aggregation Database	Europe	Sub	18486	G=0.831	A=0.168
The Genome Aggregation Database	Global	Study-wide	29960	G=0.849	A=0.150
The Genome Aggregation Database	Other	Sub	302	G=0.860	A=0.140
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.852	A=0.147
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.793	A=0.207

PMID	Title	Author	Journal
18596909	IGF-1, IGFBP-1, and IGFBP-3 polymorphisms predict circulating IGF levels but not breast cancer risk: findings from the Breast and Prostate Cancer Cohort Consortium (BPC3).	Patel AV	PLoS One
20039319	IGF1, IGFBP1, and IGFBP3 genes and mammographic density: the Multiethnic Cohort.	Verheus M	Int J Cancer
21078522	Common genetic variation within IGFI, IGFII, IGFBP-1, and IGFBP-3 and endometrial cancer risk.	McGrath M	Gynecol Oncol
19858071	Common genetic variation in IGF1, IGFBP1 and IGFBP3 and ovarian cancer risk.	Terry KL	Carcinogenesis
21314694	Genomewide association analysis of symptoms of alcohol dependence in the molecular genetics of schizophrenia (MGS2) control sample.	Kendler KS	Alcohol Clin Exp Res
22894543	Genetic variability in IGF-1 and IGFBP-3 and body size in early life.	Poole EM	BMC Public Health
25622599	Pharmacogenomics of hypertension: a genome-wide, placebo-controlled cross-over study, using four classes of antihypertensive drugs.	Hiltunen TP	J Am Heart Assoc
17300730	Common genetic variation in IGF1, IGFBP-1, and IGFBP-3 in relation to mammographic density: a cross-sectional study.	Tamimi RM	Breast Cancer Res
19551864	Genetic variation and circulating levels of IGF-I and IGFBP-3 in relation to risk of proliferative benign breast disease.	Su X	Int J Cancer

P-Value

SNP ID	p-value	Traits	Study
rs1553009	0.000154	alcohol dependence	21314694

eQTL of rs1553009 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 rs1553009 in Fetal Brain

Probe ID	Position	Gene	beta	p-value
There is no meQTL annotation for this SNP

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 )
chr7	45929241	45929338	E073	20247

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr7	45927783	45929212	E067	18789
chr7	45927783	45929212	E068	18789
chr7	45927783	45929212	E072	18789
chr7	45927783	45929212	E073	18789
chr7	45927783	45929212	E082	18789
chr7	45957108	45958488	E082	48114