SNP Detail Info-rs9353016

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

LGSN : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0469 (14038/29878,GnomAD)
A=0391 (11401/29118,TOPMED)
A=0430 (2152/5008,1000G)
G==0448 (1725/3854,ALSPAC)
G==0449 (1664/3708,TWINSUK)

Position: chr6:63476127 (GRCh38.p7) (6q12)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 0 Enhancer around

Promoter: 0 Promoter around

Sequence Name	Change(s)
GRCh38.p7 chr 6	NC_000006.12:g.63476127G>A
GRCh37.p13 chr 6	NC_000006.11:g.64186032G>A

Molecule type	Change	Amino acid[Codon]	SO Term
LGSN transcript variant 2	NM_001143940.1:c.	N/A	Genic Upstream Transcript Variant
LGSN transcript variant 1	NM_016571.2:c.	N/A	Genic Upstream Transcript Variant
LGSN transcript variant X1	XM_017010929.1:c.	N/A	Intron Variant
LGSN transcript variant X2	XM_011535889.2:c.	N/A	Genic Upstream Transcript Variant
LGSN transcript variant X4	XM_011535892.2:c.	N/A	Genic Upstream Transcript Variant
LGSN transcript variant X3	XM_017010930.1:c.	N/A	Genic Upstream Transcript Variant
LGSN transcript variant X5	XM_017010931.1:c.	N/A	Genic Upstream Transcript Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.812	A=0.188
1000Genomes	American	Sub	694	G=0.580	A=0.420
1000Genomes	East Asian	Sub	1008	G=0.453	A=0.547
1000Genomes	Europe	Sub	1006	G=0.419	A=0.581
1000Genomes	Global	Study-wide	5008	G=0.570	A=0.430
1000Genomes	South Asian	Sub	978	G=0.510	A=0.490
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.448	A=0.552
The Genome Aggregation Database	African	Sub	8708	G=0.775	A=0.225
The Genome Aggregation Database	American	Sub	834	G=0.580	A=0.420
The Genome Aggregation Database	East Asian	Sub	1616	G=0.456	A=0.544
The Genome Aggregation Database	Europe	Sub	18422	G=0.421	A=0.578
The Genome Aggregation Database	Global	Study-wide	29878	G=0.530	A=0.469
The Genome Aggregation Database	Other	Sub	298	G=0.370	A=0.630
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.608	A=0.391
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.449	A=0.551

PMID	Title	Author	Journal
22096494	A novel, functional and replicable risk gene region for alcohol dependence identified by genome-wide association study.	Zuo L	PLoS One

SNP ID	p-value	Traits	Study
rs9353016	1E-05	alcohol dependence	22096494

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr6:64186032	LGSN	ENSG00000146166.12	G>A	1.9599e-12	156150	Brain_Spinal_cord_cervical

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

rs9353016