rs17405217

Organism: Homo sapiens

Alleles: C>G / C>T

Gene : Feature

IREB2 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0226 (6717/29628,GnomAD)
T=0153 (767/5008,1000G)
T=0319 (1228/3854,ALSPAC)
T=0325 (1204/3708,TWINSUK)

Position: chr15:78438807 (GRCh38.p7) (15q25.1)

Phenotype: ND

Dataset:

GWASdb2

Publications: 7 publication(s)

Genomic View: See rs on genome

Enhancer: 0 Enhancer around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 15	NC_000015.10:g.78438807C>G
GRCh38.p7 chr 15	NC_000015.10:g.78438807C>T
GRCh37.p13 chr 15	NC_000015.9:g.78731149C>G
GRCh37.p13 chr 15	NC_000015.9:g.78731149C>T

Gene: IREB2, iron responsive element binding protein 2(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
IREB2 transcript variant 2	NM_001320941.1:c.	N/A	Intron Variant
IREB2 transcript variant 4	NM_001320943.1:c.	N/A	Intron Variant
IREB2 transcript variant 1	NM_004136.3:c.	N/A	Intron Variant
IREB2 transcript variant 3	NM_001320942.1:c.	N/A	5 Prime UTR Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.978	T=0.022
1000Genomes	American	Sub	694	C=0.800	T=0.200
1000Genomes	East Asian	Sub	1008	C=0.959	T=0.041
1000Genomes	Europe	Sub	1006	C=0.630	T=0.370
1000Genomes	Global	Study-wide	5008	C=0.847	T=0.153
1000Genomes	South Asian	Sub	978	C=0.810	T=0.190
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.681	T=0.319
The Genome Aggregation Database	African	Sub	8680	C=0.946	G=0.000
The Genome Aggregation Database	American	Sub	836	C=0.810	G=0.00,
The Genome Aggregation Database	East Asian	Sub	1620	C=0.964	G=0.000
The Genome Aggregation Database	Europe	Sub	18190	C=0.674	G=0.000
The Genome Aggregation Database	Global	Study-wide	29628	C=0.773	G=0.000
The Genome Aggregation Database	Other	Sub	302	C=0.650	G=0.00,
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.675	T=0.325

PMID	Title	Author	Journal
26981579	Gene by Environment Investigation of Incident Lung Cancer Risk in African-Americans.	David SP	EBioMedicine
18759969	In search of causal variants: refining disease association signals using cross-population contrasts.	Saccone NL	BMC Genet
23221128	Fine-mapping of the 5p15.33, 6p22.1-p21.31, and 15q25.1 regions identifies functional and histology-specific lung cancer susceptibility loci in African-Americans.	Walsh KM	Cancer Epidemiol Biomarkers Prev
20624154	Incorporating age at onset of smoking into genetic models for nicotine dependence: evidence for interaction with multiple genes.	Grucza RA	Addict Biol
19706762	The CHRNA5-CHRNA3-CHRNB4 nicotinic receptor subunit gene cluster affects risk for nicotine dependence in African-Americans and in European-Americans.	Saccone NL	Cancer Res
17158188	Novel genes identified in a high-density genome wide association study for nicotine dependence.	Bierut LJ	Hum Mol Genet
19259974	Multiple distinct risk loci for nicotine dependence identified by dense coverage of the complete family of nicotinic receptor subunit (CHRN) genes.	Saccone NL	Am J Med Genet B Neuropsychiatr Genet

P-Value

SNP ID	p-value	Traits	Study
rs17405217	0.000595	nicotine dependence	17158188

eQTL of rs17405217 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr15:78731149	CHRNA5	ENSG00000169684.9	C>T	1.6230e-20	-126713	Cortex
Chr15:78731149	CHRNA5	ENSG00000169684.9	C>T	1.5335e-14	-126713	Caudate_basal_ganglia
Chr15:78731149	CHRNA5	ENSG00000169684.9	C>T	5.1270e-15	-126713	Nucleus_accumbens_basal_ganglia

meQTL of rs17405217 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.