rs6429856

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

LRP1B : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G==0446 (13290/29768,GnomAD)
G==0457 (13333/29118,TOPMED)
G==0477 (2389/5008,1000G)
G==0394 (1519/3854,ALSPAC)
G==0405 (1500/3708,TWINSUK)

Position: chr2:141022386 (GRCh38.p7) (2q22.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 50 Enhancers around

Promoter: 3 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.141022386G>A
GRCh37.p13 chr 2	NC_000002.11:g.141779955G>A

Gene: LRP1B, LDL receptor related protein 1B(minus strand)

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

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.567	A=0.433
1000Genomes	American	Sub	694	G=0.360	A=0.640
1000Genomes	East Asian	Sub	1008	G=0.453	A=0.547
1000Genomes	Europe	Sub	1006	G=0.454	A=0.546
1000Genomes	Global	Study-wide	5008	G=0.477	A=0.523
1000Genomes	South Asian	Sub	978	G=0.490	A=0.510
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.394	A=0.606
The Genome Aggregation Database	African	Sub	8704	G=0.551	A=0.449
The Genome Aggregation Database	American	Sub	830	G=0.360	A=0.640
The Genome Aggregation Database	East Asian	Sub	1574	G=0.465	A=0.535
The Genome Aggregation Database	Europe	Sub	18358	G=0.398	A=0.601
The Genome Aggregation Database	Global	Study-wide	29768	G=0.446	A=0.553
The Genome Aggregation Database	Other	Sub	302	G=0.470	A=0.530
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.457	A=0.542
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.405	A=0.595

PMID	Title	Author	Journal
24277619	ALDH2 is associated to alcohol dependence and is the major genetic determinant of "daily maximum drinks" in a GWAS study of an isolated rural Chinese sample.	Quillen EE	Am J Med Genet B Neuropsychiatr Genet

P-Value

SNP ID	p-value	Traits	Study
rs6429856	0.000592	alcohol consumption (maxi-drinks)	24277619

eQTL of rs6429856 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 rs6429856 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.

Enhancer Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr2	141772350	141772451	E067	-7504
chr2	141772496	141772549	E067	-7406
chr2	141772778	141772946	E067	-7009
chr2	141773331	141773485	E067	-6470
chr2	141773522	141773600	E067	-6355
chr2	141819701	141819897	E067	39746
chr2	141820132	141820318	E067	40177
chr2	141820599	141820650	E067	40644
chr2	141821114	141821193	E067	41159
chr2	141772350	141772451	E068	-7504
chr2	141772496	141772549	E068	-7406
chr2	141773022	141773206	E068	-6749
chr2	141773331	141773485	E068	-6470
chr2	141773522	141773600	E068	-6355
chr2	141773022	141773206	E069	-6749
chr2	141773331	141773485	E069	-6470
chr2	141773522	141773600	E069	-6355
chr2	141774280	141774370	E069	-5585
chr2	141819701	141819897	E069	39746
chr2	141820132	141820318	E069	40177
chr2	141753537	141753614	E070	-26341
chr2	141753989	141754033	E070	-25922
chr2	141754198	141754387	E070	-25568
chr2	141772350	141772451	E071	-7504
chr2	141772496	141772549	E071	-7406
chr2	141772778	141772946	E071	-7009
chr2	141773022	141773206	E071	-6749
chr2	141773331	141773485	E071	-6470
chr2	141773522	141773600	E071	-6355
chr2	141774280	141774370	E071	-5585
chr2	141819701	141819897	E071	39746
chr2	141820132	141820318	E071	40177
chr2	141820599	141820650	E071	40644
chr2	141819701	141819897	E072	39746
chr2	141773022	141773206	E073	-6749
chr2	141773331	141773485	E073	-6470
chr2	141773522	141773600	E073	-6355
chr2	141819701	141819897	E073	39746
chr2	141820132	141820318	E073	40177
chr2	141772778	141772946	E074	-7009
chr2	141773022	141773206	E074	-6749
chr2	141773331	141773485	E074	-6470
chr2	141773522	141773600	E074	-6355
chr2	141819701	141819897	E074	39746
chr2	141820132	141820318	E074	40177
chr2	141759305	141759748	E081	-20207
chr2	141759305	141759748	E082	-20207
chr2	141772350	141772451	E082	-7504
chr2	141772496	141772549	E082	-7406
chr2	141772778	141772946	E082	-7009

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr2	141806583	141807037	E068	26628
chr2	141806583	141807037	E072	26628
chr2	141806583	141807037	E073	26628