rs1578405

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

PCSK2 : Intron Variant
LOC105372546 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0406 (12143/29906,GnomAD)
G=0427 (12446/29118,TOPMED)
G=0351 (1756/5008,1000G)
G=0387 (1491/3854,ALSPAC)
G=0388 (1438/3708,TWINSUK)

Position: chr20:17248099 (GRCh38.p7) (20p12.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 3 Enhancers around

Promoter: 61 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 20	NC_000020.11:g.17248099A>G
GRCh37.p13 chr 20	NC_000020.10:g.17228744A>G

Gene: PCSK2, proprotein convertase subtilisin/kexin type 2(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PCSK2 transcript variant 3	NM_001201528.1:c.	N/A	Intron Variant
PCSK2 transcript variant 2	NM_001201529.2:c.	N/A	Intron Variant
PCSK2 transcript variant 1	NM_002594.4:c.	N/A	Intron Variant

Gene: LOC105372546, uncharacterized LOC105372546(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105372546 transcript variant X2	XR_001754504.1:n.	N/A	Intron Variant
LOC105372546 transcript variant X1	XR_001754503.1:n.	N/A	Genic Downstream Transcript Variant
LOC105372546 transcript variant X3	XR_001754506.1:n.	N/A	Genic Downstream Transcript Variant
LOC105372546 transcript variant X4	XR_001754507.1:n.	N/A	Genic Downstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.498	G=0.502
1000Genomes	American	Sub	694	A=0.640	G=0.360
1000Genomes	East Asian	Sub	1008	A=0.841	G=0.159
1000Genomes	Europe	Sub	1006	A=0.598	G=0.402
1000Genomes	Global	Study-wide	5008	A=0.649	G=0.351
1000Genomes	South Asian	Sub	978	A=0.710	G=0.290
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.613	G=0.387
The Genome Aggregation Database	African	Sub	8682	A=0.505	G=0.495
The Genome Aggregation Database	American	Sub	836	A=0.600	G=0.400
The Genome Aggregation Database	East Asian	Sub	1616	A=0.860	G=0.140
The Genome Aggregation Database	Europe	Sub	18470	A=0.613	G=0.386
The Genome Aggregation Database	Global	Study-wide	29906	A=0.594	G=0.406
The Genome Aggregation Database	Other	Sub	302	A=0.550	G=0.450
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.572	G=0.427
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.612	G=0.388

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
rs1578405	0.000373	alcohol dependence	24277619

eQTL of rs1578405 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 rs1578405 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 )
chr20	17183473	17183651	E081	-45093
chr20	17267395	17267504	E082	38651
chr20	17267560	17267689	E082	38816

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr20	17206211	17206405	E067	-22339
chr20	17206421	17207872	E067	-20872
chr20	17207892	17208127	E067	-20617
chr20	17208203	17209057	E067	-19687
chr20	17209100	17209179	E067	-19565
chr20	17209194	17209644	E067	-19100
chr20	17209716	17210424	E067	-18320
chr20	17210465	17210542	E067	-18202
chr20	17206211	17206405	E068	-22339
chr20	17206421	17207872	E068	-20872
chr20	17207892	17208127	E068	-20617
chr20	17208203	17209057	E068	-19687
chr20	17209100	17209179	E068	-19565
chr20	17209194	17209644	E068	-19100
chr20	17209716	17210424	E068	-18320
chr20	17210465	17210542	E068	-18202
chr20	17206211	17206405	E069	-22339
chr20	17206421	17207872	E069	-20872
chr20	17207892	17208127	E069	-20617
chr20	17208203	17209057	E069	-19687
chr20	17209100	17209179	E069	-19565
chr20	17209194	17209644	E069	-19100
chr20	17209716	17210424	E069	-18320
chr20	17210465	17210542	E069	-18202
chr20	17206421	17207872	E070	-20872
chr20	17207892	17208127	E070	-20617
chr20	17206211	17206405	E071	-22339
chr20	17206421	17207872	E071	-20872
chr20	17207892	17208127	E071	-20617
chr20	17208203	17209057	E071	-19687
chr20	17209100	17209179	E071	-19565
chr20	17209194	17209644	E071	-19100
chr20	17206211	17206405	E072	-22339
chr20	17206421	17207872	E072	-20872
chr20	17207892	17208127	E072	-20617
chr20	17208203	17209057	E072	-19687
chr20	17209100	17209179	E072	-19565
chr20	17209194	17209644	E072	-19100
chr20	17209716	17210424	E072	-18320
chr20	17210465	17210542	E072	-18202
chr20	17206211	17206405	E073	-22339
chr20	17206421	17207872	E073	-20872
chr20	17207892	17208127	E073	-20617
chr20	17208203	17209057	E073	-19687
chr20	17209100	17209179	E073	-19565
chr20	17209194	17209644	E073	-19100
chr20	17209716	17210424	E073	-18320
chr20	17210465	17210542	E073	-18202
chr20	17206211	17206405	E074	-22339
chr20	17206421	17207872	E074	-20872
chr20	17207892	17208127	E074	-20617
chr20	17208203	17209057	E074	-19687
chr20	17209100	17209179	E074	-19565
chr20	17206211	17206405	E081	-22339
chr20	17206421	17207872	E081	-20872
chr20	17207892	17208127	E081	-20617
chr20	17206211	17206405	E082	-22339
chr20	17206421	17207872	E082	-20872
chr20	17207892	17208127	E082	-20617
chr20	17209716	17210424	E082	-18320
chr20	17210465	17210542	E082	-18202