rs12491742

Organism: Homo sapiens

Alleles: T>G

Gene : Feature

STXBP5L : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0040 (1212/29728,GnomAD)
G=0033 (986/29118,TOPMED)
G=0017 (87/5008,1000G)
G=0047 (183/3854,ALSPAC)
G=0054 (201/3708,TWINSUK)

Position: chr3:120971356 (GRCh38.p7) (3q13.33)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 0 Enhancer around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 3	NC_000003.12:g.120971356T>G
GRCh37.p13 chr 3	NC_000003.11:g.120690203T>G

Gene: STXBP5L, syntaxin binding protein 5 like(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
STXBP5L transcript variant 2	NM_001308330.1:c.	N/A	Intron Variant
STXBP5L transcript variant 1	NM_014980.2:c.	N/A	Intron Variant
STXBP5L transcript variant X1	XM_006713825.3:c.	N/A	Intron Variant
STXBP5L transcript variant X6	XM_011513328.2:c.	N/A	Intron Variant
STXBP5L transcript variant X6	XM_011513331.2:c.	N/A	Intron Variant
STXBP5L transcript variant X12	XM_011513333.2:c.	N/A	Intron Variant
STXBP5L transcript variant X2	XM_017007530.1:c.	N/A	Intron Variant
STXBP5L transcript variant X3	XM_017007531.1:c.	N/A	Intron Variant
STXBP5L transcript variant X4	XM_017007532.1:c.	N/A	Intron Variant
STXBP5L transcript variant X4	XM_017007534.1:c.	N/A	Intron Variant
STXBP5L transcript variant X13	XM_017007535.1:c.	N/A	Intron Variant
STXBP5L transcript variant X7	XM_011513332.2:c.	N/A	Genic Upstream Transcript Variant
STXBP5L transcript variant X5	XM_017007533.1:c.	N/A	Genic Upstream Transcript Variant
STXBP5L transcript variant X5	XR_001740373.1:n.	N/A	Intron Variant
STXBP5L transcript variant X3	XR_924217.2:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=1.000	G=0.000
1000Genomes	American	Sub	694	T=0.980	G=0.020
1000Genomes	East Asian	Sub	1008	T=1.000	G=0.000
1000Genomes	Europe	Sub	1006	T=0.943	G=0.057
1000Genomes	Global	Study-wide	5008	T=0.983	G=0.017
1000Genomes	South Asian	Sub	978	T=0.990	G=0.010
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.953	G=0.047
The Genome Aggregation Database	African	Sub	8586	T=0.990	G=0.010
The Genome Aggregation Database	American	Sub	818	T=0.970	G=0.030
The Genome Aggregation Database	East Asian	Sub	1610	T=1.000	G=0.000
The Genome Aggregation Database	Europe	Sub	18414	T=0.940	G=0.059
The Genome Aggregation Database	Global	Study-wide	29728	T=0.959	G=0.040
The Genome Aggregation Database	Other	Sub	300	T=0.970	G=0.030
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.966	G=0.033
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.946	G=0.054

PMID	Title	Author	Journal
21314694	Genomewide association analysis of symptoms of alcohol dependence in the molecular genetics of schizophrenia (MGS2) control sample.	Kendler KS	Alcohol Clin Exp Res

P-Value

SNP ID	p-value	Traits	Study
rs12491742	0.00064	alcohol dependence	21314694

eQTL of rs12491742 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
There is no eQTL annotation for this SNP

meQTL of rs12491742 in Fetal Brain

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

Genomic View

Chromatin Interaction

There is no significant Hi-C chromatin interaction data for this SNP.