SNP Detail Info-rs1468900

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

LOC105374811 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0168 (5036/29954,GnomAD)
G=0195 (5690/29116,TOPMED)
G=0237 (1185/5008,1000G)
G=0089 (342/3854,ALSPAC)
G=0089 (329/3708,TWINSUK)

Position: chr2:75222857 (GRCh38.p7) (2p12)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 5 Enhancers around

Promoter: 6 Promoters around

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.75222857A>G
GRCh37.p13 chr 2	NC_000002.11:g.75449983A>G

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105374811 transcript variant X1	XM_017005462.1:c.	N/A	Intron Variant
LOC105374811 transcript variant X2	XM_017005463.1:c.	N/A	Intron Variant
LOC105374811 transcript variant X3	XR_940257.2:n.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.669	G=0.331
1000Genomes	American	Sub	694	A=0.880	G=0.120
1000Genomes	East Asian	Sub	1008	A=0.706	G=0.294
1000Genomes	Europe	Sub	1006	A=0.909	G=0.091
1000Genomes	Global	Study-wide	5008	A=0.763	G=0.237
1000Genomes	South Asian	Sub	978	A=0.720	G=0.280
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.911	G=0.089
The Genome Aggregation Database	African	Sub	8708	A=0.698	G=0.302
The Genome Aggregation Database	American	Sub	838	A=0.870	G=0.130
The Genome Aggregation Database	East Asian	Sub	1610	A=0.686	G=0.314
The Genome Aggregation Database	Europe	Sub	18496	A=0.904	G=0.096
The Genome Aggregation Database	Global	Study-wide	29954	A=0.831	G=0.168
The Genome Aggregation Database	Other	Sub	302	A=0.940	G=0.060
Trans-Omics for Precision Medicine	Global	Study-wide	29116	A=0.804	G=0.195
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.911	G=0.089

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
rs1468900	0.000132	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 )
chr2	75449770	75449908	E070	-75
chr2	75429257	75429307	E081	-20676
chr2	75478791	75478874	E081	28808
chr2	75478947	75479001	E081	28964
chr2	75479057	75479630	E081	29074

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr2	75426407	75428337	E067	-21646
chr2	75426407	75428337	E068	-21646
chr2	75426407	75428337	E072	-21646
chr2	75426407	75428337	E073	-21646
chr2	75426407	75428337	E074	-21646
chr2	75426407	75428337	E082	-21646

rs1468900