rs1668589

Homo sapiens
A>G
PLA2G4D : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
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)
chr15:42071571 (GRCh38.p7) (15q15.1)
AD
GWASdb2
2   publication(s)
See rs on genome
51 Enhancers around
0 Promoter around

Genomic Coordinates

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

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

Molecule type Change Amino acid[Codon] SO Term
PLA2G4D transcriptNM_178034.3:c.N/AIntron Variant
PLA2G4D transcript variant X1XM_011521467.2:c.N/AIntron Variant
PLA2G4D transcript variant X2XR_931798.2:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322A=0.493G=0.507
1000GenomesAmericanSub694A=0.210G=0.790
1000GenomesEast AsianSub1008A=0.417G=0.583
1000GenomesEuropeSub1006A=0.236G=0.764
1000GenomesGlobalStudy-wide5008A=0.360G=0.640
1000GenomesSouth AsianSub978A=0.360G=0.640
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.234G=0.766
The Exome Aggregation ConsortiumAmericanSub21896A=0.312G=0.687
The Exome Aggregation ConsortiumAsianSub24098A=0.372G=0.627
The Exome Aggregation ConsortiumEuropeSub72906A=0.210G=0.789
The Exome Aggregation ConsortiumGlobalStudy-wide119792A=0.261G=0.738
The Exome Aggregation ConsortiumOtherSub892A=0.230G=0.770
The Genome Aggregation DatabaseAfricanSub8684A=0.426G=0.574
The Genome Aggregation DatabaseAmericanSub838A=0.230G=0.770
The Genome Aggregation DatabaseEast AsianSub1614A=0.416G=0.584
The Genome Aggregation DatabaseEuropeSub18406A=0.206G=0.793
The Genome Aggregation DatabaseGlobalStudy-wide29844A=0.282G=0.717
The Genome Aggregation DatabaseOtherSub302A=0.210G=0.790
Trans-Omics for Precision MedicineGlobalStudy-wide29118A=0.309G=0.690
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.202G=0.798
PMID Title Author Journal
18686860[Study on the genetic association between the polymorphism of cytosolic phospholipase A2 family genes and schizophrenia].Yu QZhonghua Liu Xing Bing Xue Za Zhi
23743675A meta-analysis of two genome-wide association studies to identify novel loci for maximum number of alcoholic drinks.Kapoor MHum Genet

P-Value

SNP ID p-value Traits Study
rs16685890.000218alcohol consumption23743675

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

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr15:42363769PLA2G4EENSG00000188089.9A>G1.3536e-320381Caudate_basal_ganglia

meQTL of rs1668589 in Fetal Brain

Probe ID Position Gene beta p-value
cg07484808chr15:42349336-0.007735266155777569.7521e-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 )
chr154240013742400224E06736368
chr154234874442348808E068-14961
chr154235826442358384E068-5385
chr154235848442359100E069-4669
chr154236200842362058E069-1711
chr154237641242377455E06912643
chr154239863242398748E06934863
chr154239884342398961E06935074
chr154239956042400101E06935791
chr154240013742400224E06936368
chr154235723742357743E070-6026
chr154235776942357827E070-5942
chr154235826442358384E070-5385
chr154235848442359100E070-4669
chr154237507242375254E07011303
chr154237529142375358E07011522
chr154237544142375621E07011672
chr154239750342397579E07033734
chr154239760142397665E07033832
chr154239784442397901E07034075
chr154239846642398548E07034697
chr154239863242398748E07034863
chr154239884342398961E07035074
chr154239956042400101E07035791
chr154240013742400224E07036368
chr154237641242377455E07112643
chr154239217742392475E07128408
chr154239249842392571E07128729
chr154239258542392909E07128816
chr154239846642398548E07134697
chr154240013742400224E07136368
chr154235848442359100E072-4669
chr154235918742359267E072-4502
chr154237641242377455E07212643
chr154239760142397665E07233832
chr154239784442397901E07234075
chr154239846642398548E07234697
chr154240013742400224E07236368
chr154234874442348808E073-14961
chr154239956042400101E07335791
chr154240013742400224E07336368
chr154234874442348808E074-14961
chr154234302542343362E081-20407
chr154234357842343634E081-20135
chr154237157442371721E0817805
chr154239956042400101E08135791
chr154240013742400224E08136368
chr154235723742357743E082-6026
chr154235776942357827E082-5942
chr154239956042400101E08235791
chr154240013742400224E08236368