SNP Detail Info-rs7558514

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

LRP1B : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G==0392 (11736/29892,GnomAD)
G==0399 (11626/29118,TOPMED)
G==0312 (1563/5008,1000G)
G==0498 (1919/3854,ALSPAC)
G==0483 (1792/3708,TWINSUK)

Position: chr2:141219604 (GRCh38.p7) (2q22.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 5 Enhancers around

Promoter: 0 Promoter around

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.141219604G>A
GRCh37.p13 chr 2	NC_000002.11:g.141977173G>A

Molecule type	Change	Amino acid[Codon]	SO Term
LRP1B transcript	NM_018557.2:c.	N/A	Intron Variant
LRP1B transcript variant X1	XM_017004341.1:c.	N/A	Intron Variant
LRP1B transcript variant X3	XM_017004342.1:c.	N/A	Genic Upstream Transcript Variant
LRP1B transcript variant X2	XR_001738778.1:n.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.258	A=0.742
1000Genomes	American	Sub	694	G=0.390	A=0.610
1000Genomes	East Asian	Sub	1008	G=0.077	A=0.923
1000Genomes	Europe	Sub	1006	G=0.495	A=0.505
1000Genomes	Global	Study-wide	5008	G=0.312	A=0.688
1000Genomes	South Asian	Sub	978	G=0.380	A=0.620
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.498	A=0.502
The Genome Aggregation Database	African	Sub	8692	G=0.284	A=0.716
The Genome Aggregation Database	American	Sub	838	G=0.410	A=0.590
The Genome Aggregation Database	East Asian	Sub	1610	G=0.068	A=0.932
The Genome Aggregation Database	Europe	Sub	18450	G=0.471	A=0.528
The Genome Aggregation Database	Global	Study-wide	29892	G=0.392	A=0.607
The Genome Aggregation Database	Other	Sub	302	G=0.420	A=0.580
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.399	A=0.600
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.483	A=0.517

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

SNP ID	p-value	Traits	Study
rs7558514	0.000112	alcohol dependence	21314694

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	141944231	141945045	E067	-32128
chr2	141999272	141999454	E071	22099
chr2	141944231	141945045	E074	-32128
chr2	142001924	142001979	E074	24751
chr2	141980683	141980861	E081	3510

rs7558514