SNP Detail Info-rs1017454

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

LOC105374658 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0288 (8611/29862,GnomAD)
A=0286 (8344/29118,TOPMED)
A=0274 (1372/5008,1000G)
A=0388 (1495/3854,ALSPAC)
A=0376 (1396/3708,TWINSUK)

Position: chr5:12975210 (GRCh38.p7) (5p15.2)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 0 Enhancer around

Promoter: 0 Promoter around

Sequence Name	Change(s)
GRCh38.p7 chr 5	NC_000005.10:g.12975210G>A
GRCh37.p13 chr 5	NC_000005.9:g.12975322G>A

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105374658 transcript variant X3	XR_001742602.1:n.	N/A	Intron Variant
LOC105374658 transcript variant X1	XR_925796.2:n.	N/A	Intron Variant
LOC105374658 transcript variant X2	XR_925797.2:n.	N/A	Genic Downstream Transcript Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.879	A=0.121
1000Genomes	American	Sub	694	G=0.590	A=0.410
1000Genomes	East Asian	Sub	1008	G=0.760	A=0.240
1000Genomes	Europe	Sub	1006	G=0.653	A=0.347
1000Genomes	Global	Study-wide	5008	G=0.726	A=0.274
1000Genomes	South Asian	Sub	978	G=0.660	A=0.340
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.612	A=0.388
The Genome Aggregation Database	African	Sub	8710	G=0.845	A=0.155
The Genome Aggregation Database	American	Sub	832	G=0.600	A=0.400
The Genome Aggregation Database	East Asian	Sub	1608	G=0.758	A=0.242
The Genome Aggregation Database	Europe	Sub	18410	G=0.651	A=0.348
The Genome Aggregation Database	Global	Study-wide	29862	G=0.711	A=0.288
The Genome Aggregation Database	Other	Sub	302	G=0.620	A=0.380
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.713	A=0.286
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.624	A=0.376

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
rs1017454	0.00028	alcohol dependence	20201924
rs1017454	0.0009	alcohol dependence(early age of onset)	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

rs1017454