rs1668589

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

PLA2G4D : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A==0261 (31366/119792,ExAC)
A==0282 (8426/29844,GnomAD)
A==0309 (9000/29118,TOPMED)
G=0289 (3763/13004,GO-ESP)
A==0360 (1802/5008,1000G)
A==0234 (903/3854,ALSPAC)
A==0202 (749/3708,TWINSUK)

Position: chr15:42071571 (GRCh38.p7) (15q15.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 2 publication(s)

Genomic View: See rs on genome

Enhancer: 51 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 15	NC_000015.10:g.42071571A>G
GRCh37.p13 chr 15	NC_000015.9:g.42363769A>G

Gene: PLA2G4D, phospholipase A2 group IVD(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PLA2G4D transcript	NM_178034.3:c.	N/A	Intron Variant
PLA2G4D transcript variant X1	XM_011521467.2:c.	N/A	Intron Variant
PLA2G4D transcript variant X2	XR_931798.2:n.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.493	G=0.507
1000Genomes	American	Sub	694	A=0.210	G=0.790
1000Genomes	East Asian	Sub	1008	A=0.417	G=0.583
1000Genomes	Europe	Sub	1006	A=0.236	G=0.764
1000Genomes	Global	Study-wide	5008	A=0.360	G=0.640
1000Genomes	South Asian	Sub	978	A=0.360	G=0.640
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.234	G=0.766
The Exome Aggregation Consortium	American	Sub	21896	A=0.312	G=0.687
The Exome Aggregation Consortium	Asian	Sub	24098	A=0.372	G=0.627
The Exome Aggregation Consortium	Europe	Sub	72906	A=0.210	G=0.789
The Exome Aggregation Consortium	Global	Study-wide	119792	A=0.261	G=0.738
The Exome Aggregation Consortium	Other	Sub	892	A=0.230	G=0.770
The Genome Aggregation Database	African	Sub	8684	A=0.426	G=0.574
The Genome Aggregation Database	American	Sub	838	A=0.230	G=0.770
The Genome Aggregation Database	East Asian	Sub	1614	A=0.416	G=0.584
The Genome Aggregation Database	Europe	Sub	18406	A=0.206	G=0.793
The Genome Aggregation Database	Global	Study-wide	29844	A=0.282	G=0.717
The Genome Aggregation Database	Other	Sub	302	A=0.210	G=0.790
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.309	G=0.690
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.202	G=0.798

PMID	Title	Author	Journal
18686860	[Study on the genetic association between the polymorphism of cytosolic phospholipase A2 family genes and schizophrenia].	Yu Q	Zhonghua Liu Xing Bing Xue Za Zhi
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
rs1668589	0.000218	alcohol consumption	23743675

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr15:42363769	PLA2G4E	ENSG00000188089.9	A>G	1.3536e-3	20381	Caudate_basal_ganglia

Probe ID	Position	Gene	beta	p-value
cg07484808	chr15:42349336		-0.00773526615577756	9.7521e-14

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 )
chr15	42400137	42400224	E067	36368
chr15	42348744	42348808	E068	-14961
chr15	42358264	42358384	E068	-5385
chr15	42358484	42359100	E069	-4669
chr15	42362008	42362058	E069	-1711
chr15	42376412	42377455	E069	12643
chr15	42398632	42398748	E069	34863
chr15	42398843	42398961	E069	35074
chr15	42399560	42400101	E069	35791
chr15	42400137	42400224	E069	36368
chr15	42357237	42357743	E070	-6026
chr15	42357769	42357827	E070	-5942
chr15	42358264	42358384	E070	-5385
chr15	42358484	42359100	E070	-4669
chr15	42375072	42375254	E070	11303
chr15	42375291	42375358	E070	11522
chr15	42375441	42375621	E070	11672
chr15	42397503	42397579	E070	33734
chr15	42397601	42397665	E070	33832
chr15	42397844	42397901	E070	34075
chr15	42398466	42398548	E070	34697
chr15	42398632	42398748	E070	34863
chr15	42398843	42398961	E070	35074
chr15	42399560	42400101	E070	35791
chr15	42400137	42400224	E070	36368
chr15	42376412	42377455	E071	12643
chr15	42392177	42392475	E071	28408
chr15	42392498	42392571	E071	28729
chr15	42392585	42392909	E071	28816
chr15	42398466	42398548	E071	34697
chr15	42400137	42400224	E071	36368
chr15	42358484	42359100	E072	-4669
chr15	42359187	42359267	E072	-4502
chr15	42376412	42377455	E072	12643
chr15	42397601	42397665	E072	33832
chr15	42397844	42397901	E072	34075
chr15	42398466	42398548	E072	34697
chr15	42400137	42400224	E072	36368
chr15	42348744	42348808	E073	-14961
chr15	42399560	42400101	E073	35791
chr15	42400137	42400224	E073	36368
chr15	42348744	42348808	E074	-14961
chr15	42343025	42343362	E081	-20407
chr15	42343578	42343634	E081	-20135
chr15	42371574	42371721	E081	7805
chr15	42399560	42400101	E081	35791
chr15	42400137	42400224	E081	36368
chr15	42357237	42357743	E082	-6026
chr15	42357769	42357827	E082	-5942
chr15	42399560	42400101	E082	35791
chr15	42400137	42400224	E082	36368

rs1668589

Genomic Coordinates

Gene: PLA2G4D, phospholipase A2 group IVD(minus strand)

Population Frequency

P-Value

eQTL of rs1668589 in Brain tissues (GTEx Analysis Release V7)

meQTL of rs1668589 in Fetal Brain

Genomic View

Chromatin Interaction

Enhancer Annotation (GRCh37.p13)