SNP Detail Info-rs17343066

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

SLC28A3 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0386 (11573/29914,GnomAD)
A=0357 (10396/29118,TOPMED)
A=0343 (1720/5008,1000G)
G==0472 (1820/3854,ALSPAC)
G==0462 (1714/3708,TWINSUK)

Position: chr9:84331158 (GRCh38.p7) (9q21.33)

Phenotype: ND

Dataset:

GWASdb2

Publications: 3 publication(s)

Genomic View: See rs on genome

Enhancer: 15 Enhancers around

Promoter: 0 Promoter around

Sequence Name	Change(s)
GRCh38.p7 chr 9	NC_000009.12:g.84331158G>A
GRCh37.p13 chr 9	NC_000009.11:g.86946073G>A

Molecule type	Change	Amino acid[Codon]	SO Term
SLC28A3 transcript variant 1	NM_001199633.1:c.	N/A	Intron Variant
SLC28A3 transcript variant 2	NM_022127.2:c.	N/A	Intron Variant
SLC28A3 transcript variant 3	NR_037638.2:n.	N/A	Intron Variant
SLC28A3 transcript variant X1	XM_011518905.2:c.	N/A	Intron Variant
SLC28A3 transcript variant X2	XM_011518906.2:c.	N/A	Intron Variant
SLC28A3 transcript variant X3	XM_011518907.2:c.	N/A	Intron Variant
SLC28A3 transcript variant X6	XM_011518909.2:c.	N/A	Intron Variant
SLC28A3 transcript variant X7	XM_011518910.2:c.	N/A	Intron Variant
SLC28A3 transcript variant X5	XM_011518908.2:c.	N/A	Genic Upstream Transcript Variant
SLC28A3 transcript variant X4	XR_929832.2:n.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.913	A=0.087
1000Genomes	American	Sub	694	G=0.510	A=0.490
1000Genomes	East Asian	Sub	1008	G=0.688	A=0.312
1000Genomes	Europe	Sub	1006	G=0.455	A=0.545
1000Genomes	Global	Study-wide	5008	G=0.657	A=0.343
1000Genomes	South Asian	Sub	978	G=0.590	A=0.410
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.472	A=0.528
The Genome Aggregation Database	African	Sub	8712	G=0.847	A=0.153
The Genome Aggregation Database	American	Sub	838	G=0.500	A=0.500
The Genome Aggregation Database	East Asian	Sub	1606	G=0.675	A=0.325
The Genome Aggregation Database	Europe	Sub	18456	G=0.505	A=0.495
The Genome Aggregation Database	Global	Study-wide	29914	G=0.613	A=0.386
The Genome Aggregation Database	Other	Sub	302	G=0.450	A=0.550
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.643	A=0.357
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.462	A=0.538

PMID	Title	Author	Journal
19268276	Genome-wide association study of smoking initiation and current smoking.	Vink JM	Am J Hum Genet
22173087	Gemcitabine metabolic pathway genetic polymorphisms and response in patients with non-small cell lung cancer.	Li L	Pharmacogenet Genomics
19898621	Gemcitabine and arabinosylcytosin pharmacogenomics: genome-wide association and drug response biomarkers.	Li L	PLoS One

SNP ID	p-value	Traits	Study
rs17343066	6.5E-05	nicotine smoking	19268276

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

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

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr9	86898878	86899442	E068	-46631
chr9	86899555	86899764	E068	-46309
chr9	86938775	86939243	E068	-6830
chr9	86898878	86899442	E069	-46631
chr9	86899555	86899764	E069	-46309
chr9	86899767	86899821	E069	-46252
chr9	86898447	86898497	E070	-47576
chr9	86899555	86899764	E070	-46309
chr9	86899767	86899821	E070	-46252
chr9	86898878	86899442	E071	-46631
chr9	86938775	86939243	E071	-6830
chr9	86989027	86989674	E071	42954
chr9	86989027	86989674	E072	42954
chr9	86989705	86989768	E072	43632
chr9	86930120	86930552	E074	-15521

rs17343066