SNP Detail Info-rs4398388

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

LINC00693 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0314 (9366/29814,GnomAD)
A=0380 (11077/29118,TOPMED)
A=0344 (1722/5008,1000G)
A=0188 (725/3854,ALSPAC)
A=0187 (692/3708,TWINSUK)

Position: chr3:28695131 (GRCh38.p7) (3p24.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 7 Enhancers around

Promoter: 0 Promoter around

Sequence Name	Change(s)
GRCh38.p7 chr 3	NC_000003.12:g.28695131G>A
GRCh37.p13 chr 3	NC_000003.11:g.28736622G>A

Molecule type	Change	Amino acid[Codon]	SO Term
LINC00693 transcript	NR_038840.1:n.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.353	A=0.647
1000Genomes	American	Sub	694	G=0.730	A=0.270
1000Genomes	East Asian	Sub	1008	G=0.745	A=0.255
1000Genomes	Europe	Sub	1006	G=0.785	A=0.215
1000Genomes	Global	Study-wide	5008	G=0.656	A=0.344
1000Genomes	South Asian	Sub	978	G=0.790	A=0.210
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.812	A=0.188
The Genome Aggregation Database	African	Sub	8666	G=0.409	A=0.591
The Genome Aggregation Database	American	Sub	832	G=0.690	A=0.310
The Genome Aggregation Database	East Asian	Sub	1594	G=0.696	A=0.304
The Genome Aggregation Database	Europe	Sub	18420	G=0.810	A=0.189
The Genome Aggregation Database	Global	Study-wide	29814	G=0.685	A=0.314
The Genome Aggregation Database	Other	Sub	302	G=0.920	A=0.080
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.619	A=0.380
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.813	A=0.187

PMID	Title	Author	Journal
20201924	Genome-wide association study of alcohol dependence implicates a region on chromosome 11.	Edenberg HJ	Alcohol Clin Exp Res

SNP ID	p-value	Traits	Study
rs4398388	0.000148	alcohol dependence	20201924

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 )
chr3	28709221	28709888	E067	-26734
chr3	28709221	28709888	E068	-26734
chr3	28709221	28709888	E073	-26734
chr3	28709221	28709888	E074	-26734
chr3	28784909	28785023	E081	48287
chr3	28785110	28785172	E081	48488
chr3	28785229	28785631	E081	48607

rs4398388