SNP Detail Info-rs1522016

Organism: Homo sapiens

Alleles: A>C

Gene : Feature

LOC105370301 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C=0078 (2353/29928,GnomAD)
C=0086 (2511/29118,TOPMED)
C=0074 (370/5008,1000G)
C=0105 (405/3854,ALSPAC)
C=0103 (381/3708,TWINSUK)

Position: chr13:87008539 (GRCh38.p7) (13q31.1)

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 13	NC_000013.11:g.87008539A>C
GRCh37.p13 chr 13	NC_000013.10:g.87660794A>C

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105370301 transcript variant X1	XR_931623.2:n.	N/A	Intron Variant
LOC105370301 transcript variant X2	XR_931624.1:n.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.923	C=0.077
1000Genomes	American	Sub	694	A=0.940	C=0.060
1000Genomes	East Asian	Sub	1008	A=0.967	C=0.033
1000Genomes	Europe	Sub	1006	A=0.906	C=0.094
1000Genomes	Global	Study-wide	5008	A=0.926	C=0.074
1000Genomes	South Asian	Sub	978	A=0.900	C=0.100
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.895	C=0.105
The Genome Aggregation Database	African	Sub	8728	A=0.931	C=0.069
The Genome Aggregation Database	American	Sub	836	A=0.940	C=0.060
The Genome Aggregation Database	East Asian	Sub	1618	A=0.953	C=0.047
The Genome Aggregation Database	Europe	Sub	18444	A=0.914	C=0.085
The Genome Aggregation Database	Global	Study-wide	29928	A=0.921	C=0.078
The Genome Aggregation Database	Other	Sub	302	A=0.850	C=0.150
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.913	C=0.086
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.897	C=0.103

PMID	Title	Author	Journal
23743675	A meta-analysis of two genome-wide association studies to identify novel loci for maximum number of alcoholic drinks.	Kapoor M	Hum Genet

SNP ID	p-value	Traits	Study
rs1522016	8.6E-05	alcohol consumption	23743675

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr13:87660794	SLITRK5	ENSG00000165300.6	A>C	7.2166e-3	-664076	Cerebellar_Hemisphere

Probe ID	Position	Gene	beta	p-value
There is no meQTL annotation for this SNP

rs1522016