SNP Detail Info-rs16892573

Organism: Homo sapiens

Alleles: G>A / G>C

Gene : Feature

PARK2 : Intron Variant
LOC105378098 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0022 (683/29990,GnomAD)
A=0031 (915/29118,TOPMED)
A=0028 (140/5008,1000G)
A=0011 (44/3854,ALSPAC)
A=0010 (37/3708,TWINSUK)

Position: chr6:161475487 (GRCh38.p7) (6q26)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 6 Enhancers around

Promoter: 0 Promoter around

Molecule type	Change	Amino acid[Codon]	SO Term
PRKN transcript variant 1	NM_004562.2:c.	N/A	Intron Variant
PRKN transcript variant 2	NM_013987.2:c.	N/A	Intron Variant
PRKN transcript variant 3	NM_013988.2:c.	N/A	Intron Variant
PRKN transcript variant X2	XM_011535863.1:c.	N/A	Intron Variant
PRKN transcript variant X1	XM_017010908.1:c.	N/A	Intron Variant
PARK2 transcript variant X3	XM_017010909.1:c.	N/A	Intron Variant
PARK2 transcript variant X4	XR_001743443.1:n.	N/A	Intron Variant

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105378098 transcript variant 1	NR_134593.1:n.	N/A	Intron Variant
LOC105378098 transcript variant 2	NR_134594.1:n.	N/A	Intron Variant
LOC105378098 transcript variant 3	NR_134595.1:n.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.937	A=0.063
1000Genomes	American	Sub	694	G=0.970	A=0.030
1000Genomes	East Asian	Sub	1008	G=1.000	A=0.000
1000Genomes	Europe	Sub	1006	G=0.992	A=0.008
1000Genomes	Global	Study-wide	5008	G=0.972	A=0.028
1000Genomes	South Asian	Sub	978	G=0.970	A=0.030
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.989	A=0.011
The Genome Aggregation Database	African	Sub	8726	G=0.941	A=0.059
The Genome Aggregation Database	American	Sub	838	G=0.990	A=0.01,
The Genome Aggregation Database	East Asian	Sub	1622	G=0.996	A=0.004
The Genome Aggregation Database	Europe	Sub	18502	G=0.992	A=0.007
The Genome Aggregation Database	Global	Study-wide	29990	G=0.977	A=0.022
The Genome Aggregation Database	Other	Sub	302	G=0.990	A=0.01,
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.968	A=0.031
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.990	A=0.010

PMID	Title	Author	Journal
19268276	Genome-wide association study of smoking initiation and current smoking.	Vink JM	Am J Hum Genet

SNP ID	p-value	Traits	Study
rs16892573	0.000616	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 )
chr6	10173470	10174146	E068	-24785
chr6	10173299	10173358	E070	-25573
chr6	10173470	10174146	E070	-24785
chr6	10217502	10217619	E070	18571
chr6	10217738	10217860	E070	18807
chr6	10218210	10218318	E070	19279

rs16892573