SNP Detail Info-rs319920

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

EYS : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0499 (14936/29930,GnomAD)
A==0419 (12217/29118,TOPMED)
A==0432 (2161/5008,1000G)
G=0411 (1583/3854,ALSPAC)
G=0423 (1568/3708,TWINSUK)

Position: chr6:63794359 (GRCh38.p7) (6q12)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 16 Enhancers around

Promoter: 0 Promoter around

Molecule type	Change	Amino acid[Codon]	SO Term
EYS transcript variant 1	NM_001142800.1:c.	N/A	Intron Variant
EYS transcript variant 4	NM_001292009.1:c.	N/A	Intron Variant
EYS transcript variant 2	NM_001142801.1:c.	N/A	Genic Downstream Transcript Variant
EYS transcript variant 3	NM_198283.1:c.	N/A	Genic Downstream Transcript Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.210	G=0.790
1000Genomes	American	Sub	694	A=0.400	G=0.600
1000Genomes	East Asian	Sub	1008	A=0.535	G=0.465
1000Genomes	Europe	Sub	1006	A=0.606	G=0.394
1000Genomes	Global	Study-wide	5008	A=0.432	G=0.568
1000Genomes	South Asian	Sub	978	A=0.460	G=0.540
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.589	G=0.411
The Genome Aggregation Database	African	Sub	8708	A=0.244	G=0.756
The Genome Aggregation Database	American	Sub	834	A=0.430	G=0.570
The Genome Aggregation Database	East Asian	Sub	1614	A=0.540	G=0.460
The Genome Aggregation Database	Europe	Sub	18474	A=0.621	G=0.378
The Genome Aggregation Database	Global	Study-wide	29930	A=0.501	G=0.499
The Genome Aggregation Database	Other	Sub	300	A=0.510	G=0.490
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.419	G=0.580
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.577	G=0.423

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
rs319920	0.00029	alcohol dependence	22096494

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr6:64504252	LGSN	ENSG00000146166.12	A>G	1.9599e-12	474370	Brain_Spinal_cord_cervical

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

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr6	64514172	64514807	E069	9920
chr6	64515567	64516749	E069	11315
chr6	64526651	64527912	E069	22399
chr6	64514172	64514807	E071	9920
chr6	64514865	64515035	E071	10613
chr6	64515567	64516749	E071	11315
chr6	64526651	64527912	E071	22399
chr6	64514172	64514807	E074	9920
chr6	64514865	64515035	E074	10613
chr6	64515151	64515307	E074	10899
chr6	64515375	64515486	E074	11123
chr6	64523427	64523521	E081	19175
chr6	64523591	64523774	E081	19339
chr6	64524229	64524292	E081	19977
chr6	64524448	64524625	E081	20196
chr6	64526651	64527912	E081	22399

rs319920