SNP Detail Info-rs9556369

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

GPC6 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0116 (3498/29962,GnomAD)
G=0074 (2178/29118,TOPMED)
G=0220 (1104/5008,1000G)
G=0124 (478/3854,ALSPAC)
G=0134 (498/3708,TWINSUK)

Position: chr13:94399306 (GRCh38.p7) (13q31.3)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 24 Enhancers around

Promoter: 0 Promoter around

Molecule type	Change	Amino acid[Codon]	SO Term
GPC6 transcript	NM_005708.3:c.	N/A	Intron Variant
GPC6 transcript variant X1	XM_011521044.2:c.	N/A	Intron Variant
GPC6 transcript variant X2	XM_017020298.1:c.	N/A	Intron Variant
GPC6 transcript variant X3	XM_017020299.1:c.	N/A	Intron Variant
GPC6 transcript variant X4	XM_017020300.1:c.	N/A	Intron Variant
GPC6 transcript variant X5	XM_017020301.1:c.	N/A	Intron Variant
GPC6 transcript variant X6	XM_017020302.1:c.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.988	G=0.012
1000Genomes	American	Sub	694	A=0.880	G=0.120
1000Genomes	East Asian	Sub	1008	A=0.445	G=0.555
1000Genomes	Europe	Sub	1006	A=0.892	G=0.108
1000Genomes	Global	Study-wide	5008	A=0.780	G=0.220
1000Genomes	South Asian	Sub	978	A=0.650	G=0.350
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.876	G=0.124
The Genome Aggregation Database	African	Sub	8728	A=0.973	G=0.027
The Genome Aggregation Database	American	Sub	838	A=0.900	G=0.100
The Genome Aggregation Database	East Asian	Sub	1614	A=0.424	G=0.576
The Genome Aggregation Database	Europe	Sub	18480	A=0.879	G=0.120
The Genome Aggregation Database	Global	Study-wide	29962	A=0.883	G=0.116
The Genome Aggregation Database	Other	Sub	302	A=0.900	G=0.100
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.925	G=0.074
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.866	G=0.134

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
rs9556369	2.68E-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 )
chr13	95022081	95022725	E068	-28835
chr13	95085324	95086569	E068	33764
chr13	95021630	95022061	E069	-29499
chr13	95022081	95022725	E069	-28835
chr13	95036521	95037282	E069	-14278
chr13	95022081	95022725	E070	-28835
chr13	95022783	95022996	E070	-28564
chr13	95022081	95022725	E071	-28835
chr13	95022783	95022996	E071	-28564
chr13	95036106	95036358	E071	-15202
chr13	95036521	95037282	E071	-14278
chr13	95036521	95037282	E072	-14278
chr13	95087781	95087863	E072	36221
chr13	95087878	95088277	E072	36318
chr13	95088279	95088331	E072	36719
chr13	95088352	95088526	E072	36792
chr13	95022081	95022725	E074	-28835
chr13	95022783	95022996	E074	-28564
chr13	95036106	95036358	E074	-15202
chr13	95036521	95037282	E074	-14278
chr13	95005273	95006014	E081	-45546
chr13	95006105	95006159	E081	-45401
chr13	95014453	95015115	E081	-36445
chr13	95036521	95037282	E082	-14278

rs9556369