SNP Detail Info-rs3917419

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

SELE : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0341 (9938/29116,TOPMED)
A=0350 (10160/28950,GnomAD)
A=0278 (1393/5008,1000G)
A=0409 (1577/3854,ALSPAC)
A=0406 (1505/3708,TWINSUK)

Position: chr1:169730678 (GRCh38.p7) (1q24.2)

Phenotype: AD

Dataset:

GWASdb2

Publications: 3 publication(s)

Genomic View: See rs on genome

Enhancer: 3 Enhancers around

Promoter: 7 Promoters around

Molecule type	Change	Amino acid[Codon]	SO Term
SELE transcript	NM_000450.2:c.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.751	A=0.249
1000Genomes	American	Sub	694	G=0.650	A=0.350
1000Genomes	East Asian	Sub	1008	G=0.879	A=0.121
1000Genomes	Europe	Sub	1006	G=0.610	A=0.390
1000Genomes	Global	Study-wide	5008	G=0.722	A=0.278
1000Genomes	South Asian	Sub	978	G=0.690	A=0.310
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.591	A=0.409
The Genome Aggregation Database	African	Sub	8544	G=0.718	A=0.282
The Genome Aggregation Database	American	Sub	754	G=0.660	A=0.340
The Genome Aggregation Database	East Asian	Sub	1608	G=0.856	A=0.144
The Genome Aggregation Database	Europe	Sub	17742	G=0.598	A=0.401
The Genome Aggregation Database	Global	Study-wide	28950	G=0.649	A=0.350
The Genome Aggregation Database	Other	Sub	302	G=0.530	A=0.470
Trans-Omics for Precision Medicine	Global	Study-wide	29116	G=0.658	A=0.341
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.594	A=0.406

PMID	Title	Author	Journal
20201924	Genome-wide association study of alcohol dependence implicates a region on chromosome 11.	Edenberg HJ	Alcohol Clin Exp Res
19996987	Blood pressure response to potassium supplementation is associated with genetic variation in endothelin 1 and interactions with E selectin in rural Chinese.	Montasser ME	J Hypertens
23190470	Association of SELE genotypes/haplotypes with sE-selectin levels in Taiwanese individuals: interactive effect of MMP9 level.	Wu S	BMC Med Genet

SNP ID	p-value	Traits	Study
rs3917419	0.0000243	alcoholism	pha002891
rs3917419	0.0000243	alcohol dependence	20201924

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr1:169699819	SCYL3	ENSG00000000457.9	G>A	5.6984e-7	-163589	Cerebellar_Hemisphere

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

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr1	169663053	169664067	E071	-35752
chr1	169664116	169664389	E071	-35430
chr1	169661474	169662757	E074	-37062

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	169680599	169681493	E067	-18326
chr1	169680599	169681493	E068	-18326
chr1	169680599	169681493	E069	-18326
chr1	169680599	169681493	E071	-18326
chr1	169680599	169681493	E072	-18326
chr1	169680599	169681493	E073	-18326
chr1	169680599	169681493	E074	-18326

rs3917419