SNP Detail Info-rs17078679

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

LOC105370290 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0097 (2916/29818,GnomAD)
G=0094 (2764/29118,TOPMED)
G=0113 (564/5008,1000G)
G=0066 (255/3854,ALSPAC)
G=0062 (231/3708,TWINSUK)

Position: chr13:84882257 (GRCh38.p7) (13q31.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 2 Enhancers around

Promoter: 0 Promoter around

Sequence Name	Change(s)
GRCh38.p7 chr 13	NC_000013.11:g.84882257A>G
GRCh37.p13 chr 13	NC_000013.10:g.85456392A>G

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105370290 transcript variant X2	XR_001749949.1:n.	N/A	Intron Variant
LOC105370290 transcript variant X1	XR_942135.1:n.	N/A	Intron Variant
LOC105370290 transcript variant X4	XR_942136.1:n.	N/A	Intron Variant
LOC105370290 transcript variant X3	XR_942137.1:n.	N/A	Intron Variant
LOC105370290 transcript variant X5	XR_942138.2:n.	N/A	Intron Variant
LOC105370290 transcript variant X6	XR_942139.1:n.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.845	G=0.155
1000Genomes	American	Sub	694	A=0.820	G=0.180
1000Genomes	East Asian	Sub	1008	A=0.897	G=0.103
1000Genomes	Europe	Sub	1006	A=0.925	G=0.075
1000Genomes	Global	Study-wide	5008	A=0.887	G=0.113
1000Genomes	South Asian	Sub	978	A=0.940	G=0.060
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.934	G=0.066
The Genome Aggregation Database	African	Sub	8682	A=0.865	G=0.135
The Genome Aggregation Database	American	Sub	834	A=0.840	G=0.160
The Genome Aggregation Database	East Asian	Sub	1622	A=0.922	G=0.078
The Genome Aggregation Database	Europe	Sub	18378	A=0.919	G=0.080
The Genome Aggregation Database	Global	Study-wide	29818	A=0.902	G=0.097
The Genome Aggregation Database	Other	Sub	302	A=0.960	G=0.040
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.905	G=0.094
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.938	G=0.062

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
rs17078679	0.00041	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 )
chr13	85439897	85440476	E071	-15916
chr13	85439897	85440476	E072	-15916

rs17078679