SNP Detail Info-rs9554813

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

ITGBL1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0187 (5623/29942,GnomAD)
G=0180 (5262/29118,TOPMED)
G=0239 (1199/5008,1000G)
G=0208 (800/3854,ALSPAC)
G=0210 (777/3708,TWINSUK)

Position: chr13:101639227 (GRCh38.p7) (13q33.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 1 Enhancer around

Promoter: 19 Promoters around

Sequence Name	Change(s)
GRCh38.p7 chr 13	NC_000013.11:g.101639227A>G
GRCh37.p13 chr 13	NC_000013.10:g.102291577A>G

Molecule type	Change	Amino acid[Codon]	SO Term
ITGBL1 transcript variant 4	NM_001271754.1:c.	N/A	Intron Variant
ITGBL1 transcript variant 2	NM_001271755.1:c.	N/A	Intron Variant
ITGBL1 transcript variant 3	NM_001271756.1:c.	N/A	Intron Variant
ITGBL1 transcript variant 1	NM_004791.2:c.	N/A	Intron Variant
ITGBL1 transcript variant X1	XM_005254100.4:c.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.896	G=0.104
1000Genomes	American	Sub	694	A=0.750	G=0.250
1000Genomes	East Asian	Sub	1008	A=0.574	G=0.426
1000Genomes	Europe	Sub	1006	A=0.782	G=0.218
1000Genomes	Global	Study-wide	5008	A=0.761	G=0.239
1000Genomes	South Asian	Sub	978	A=0.750	G=0.250
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.792	G=0.208
The Genome Aggregation Database	African	Sub	8720	A=0.874	G=0.126
The Genome Aggregation Database	American	Sub	836	A=0.770	G=0.230
The Genome Aggregation Database	East Asian	Sub	1614	A=0.564	G=0.436
The Genome Aggregation Database	Europe	Sub	18470	A=0.807	G=0.193
The Genome Aggregation Database	Global	Study-wide	29942	A=0.812	G=0.187
The Genome Aggregation Database	Other	Sub	302	A=0.790	G=0.210
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.819	G=0.180
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.790	G=0.210

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
rs9554813	0.00034	alcohol dependence(early age of onset)	20201924
rs9554813	0.00038	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	102333514	102333564	E081	41937

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr13	102279163	102279218	E067	-12359
chr13	102279276	102279904	E067	-11673
chr13	102279965	102280288	E067	-11289
chr13	102279163	102279218	E068	-12359
chr13	102279276	102279904	E068	-11673
chr13	102279965	102280288	E068	-11289
chr13	102279163	102279218	E069	-12359
chr13	102279276	102279904	E069	-11673
chr13	102279965	102280288	E069	-11289
chr13	102279163	102279218	E071	-12359
chr13	102279276	102279904	E071	-11673
chr13	102279965	102280288	E071	-11289
chr13	102279163	102279218	E072	-12359
chr13	102279276	102279904	E072	-11673
chr13	102279965	102280288	E072	-11289
chr13	102279965	102280288	E073	-11289
chr13	102279163	102279218	E074	-12359
chr13	102279276	102279904	E074	-11673
chr13	102279965	102280288	E074	-11289

rs9554813