rs12528857

Homo sapiens
C>A
PLA2G7 : Non Coding Transcript Variant
TDRD6 : 3 Prime UTR Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0173 (5193/29892,GnomAD)
A=0136 (3959/29118,TOPMED)
A=0143 (717/5008,1000G)
A=0230 (887/3854,ALSPAC)
A=0224 (832/3708,TWINSUK)
chr6:46702199 (GRCh38.p7) (6p12.3)
AD
GWASdb2
3   publication(s)
See rs on genome
13 Enhancers around
38 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 6NC_000006.12:g.46702199C>A
GRCh37.p13 chr 6NC_000006.11:g.46669936C>A

Gene: TDRD6, tudor domain containing 6(plus strand)

Molecule type Change Amino acid[Codon] SO Term
TDRD6 transcript variant 1NM_001010870.2:c.N/A3 Prime UTR Variant
TDRD6 transcript variant 2NM_001168359.1:c.N/A3 Prime UTR Variant

Gene: PLA2G7, phospholipase A2 group VII(minus strand)

Molecule type Change Amino acid[Codon] SO Term
PLA2G7 transcript variant 2NM_001168357.1:c.N/AGenic Downstream Transcript Variant
PLA2G7 transcript variant 1NM_005084.3:c.N/AGenic Downstream Transcript Variant
PLA2G7 transcript variant X1XM_005249408.4:c.N/AGenic Downstream Transcript Variant
PLA2G7 transcript variant X2XR_001743639.1:n....XR_001743639.1:n.3841G>TG>TNon Coding Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.983A=0.017
1000GenomesAmericanSub694C=0.850A=0.150
1000GenomesEast AsianSub1008C=0.870A=0.130
1000GenomesEuropeSub1006C=0.787A=0.213
1000GenomesGlobalStudy-wide5008C=0.857A=0.143
1000GenomesSouth AsianSub978C=0.750A=0.250
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.770A=0.230
The Genome Aggregation DatabaseAfricanSub8722C=0.947A=0.053
The Genome Aggregation DatabaseAmericanSub838C=0.850A=0.150
The Genome Aggregation DatabaseEast AsianSub1608C=0.869A=0.131
The Genome Aggregation DatabaseEuropeSub18424C=0.766A=0.233
The Genome Aggregation DatabaseGlobalStudy-wide29892C=0.826A=0.173
The Genome Aggregation DatabaseOtherSub300C=0.690A=0.310
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.864A=0.136
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.776A=0.224
PMID Title Author Journal
20201924Genome-wide association study of alcohol dependence implicates a region on chromosome 11.Edenberg HJAlcohol Clin Exp Res
20442857Genome-wide association study of Lp-PLA(2) activity and mass in the Framingham Heart Study.Suchindran SPLoS Genet
18204052Comprehensive genetic analysis of the platelet activating factor acetylhydrolase (PLA2G7) gene and cardiovascular disease in case-control and family datasets.Sutton BSHum Mol Genet

P-Value

SNP ID p-value Traits Study
rs125288570.00054alcohol dependence20201924

eQTL of rs12528857 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr6:46669936SLC25A27ENSG00000153291.11C>A2.7425e-2149258Cerebellum
Chr6:46669936TDRD6ENSG00000180113.11C>A5.8864e-2214324Cerebellum
Chr6:46669936SLC25A27ENSG00000153291.11C>A9.5972e-2149258Frontal_Cortex_BA9
Chr6:46669936TDRD6ENSG00000180113.11C>A2.9268e-1214324Frontal_Cortex_BA9
Chr6:46669936SLC25A27ENSG00000153291.11C>A1.6456e-1149258Hypothalamus
Chr6:46669936TDRD6ENSG00000180113.11C>A2.0593e-1314324Hypothalamus
Chr6:46669936SLC25A27ENSG00000153291.11C>A7.8680e-2549258Cortex
Chr6:46669936TDRD6ENSG00000180113.11C>A8.2033e-1714324Cortex
Chr6:46669936SLC25A27ENSG00000153291.11C>A4.5065e-1849258Cerebellar_Hemisphere
Chr6:46669936TDRD6ENSG00000180113.11C>A2.5099e-1514324Cerebellar_Hemisphere
Chr6:46669936SLC25A27ENSG00000153291.11C>A7.8290e-2149258Caudate_basal_ganglia
Chr6:46669936TDRD6ENSG00000180113.11C>A7.0007e-2314324Caudate_basal_ganglia
Chr6:46669936SLC25A27ENSG00000153291.11C>A4.4237e-849258Brain_Spinal_cord_cervical
Chr6:46669936SLC25A27ENSG00000153291.11C>A1.1982e-1249258Hippocampus
Chr6:46669936TDRD6ENSG00000180113.11C>A1.9740e-1014324Hippocampus
Chr6:46669936SLC25A27ENSG00000153291.11C>A4.9714e-849258Substantia_nigra
Chr6:46669936TDRD6ENSG00000180113.11C>A2.4527e-814324Substantia_nigra
Chr6:46669936SLC25A27ENSG00000153291.11C>A9.1763e-1749258Putamen_basal_ganglia
Chr6:46669936TDRD6ENSG00000180113.11C>A8.5056e-1714324Putamen_basal_ganglia
Chr6:46669936SLC25A27ENSG00000153291.11C>A7.0727e-1849258Anterior_cingulate_cortex
Chr6:46669936TDRD6ENSG00000180113.11C>A2.1831e-714324Anterior_cingulate_cortex
Chr6:46669936SLC25A27ENSG00000153291.11C>A2.6897e-1549258Nucleus_accumbens_basal_ganglia
Chr6:46669936TDRD6ENSG00000180113.11C>A3.0004e-1214324Nucleus_accumbens_basal_ganglia
Chr6:46669936SLC25A27ENSG00000153291.11C>A2.7192e-1149258Amygdala
Chr6:46669936TDRD6ENSG00000180113.11C>A2.0235e-514324Amygdala

meQTL of rs12528857 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 )
chr64662921446629520E068-40416
chr64667245646672670E0682520
chr64668691646687132E06816980
chr64664197046642744E069-27192
chr64664480846644913E070-25023
chr64664491546645010E070-24926
chr64664506646645253E070-24683
chr64664144146641555E071-28381
chr64664197046642744E071-27192
chr64667245646672670E0732520
chr64664197046642744E074-27192
chr64664480846644913E082-25023
chr64664491546645010E082-24926







Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr64662211146622173E067-47763
chr64670167946702160E06731743
chr64670221046702345E06732274
chr64670237046702461E06732434
chr64670249646703621E06732560
chr64662211146622173E068-47763
chr64662292846622978E068-46958
chr64670221046702345E06832274
chr64670237046702461E06832434
chr64670249646703621E06832560
chr64670221046702345E06932274
chr64670237046702461E06932434
chr64670249646703621E06932560
chr64670221046702345E07032274
chr64670237046702461E07032434
chr64670249646703621E07032560
chr64662211146622173E071-47763
chr64670167946702160E07131743
chr64670221046702345E07132274
chr64670237046702461E07132434
chr64670249646703621E07132560
chr64662211146622173E072-47763
chr64662292846622978E072-46958
chr64670221046702345E07232274
chr64670237046702461E07232434
chr64670249646703621E07232560
chr64662211146622173E073-47763
chr64662292846622978E073-46958
chr64670221046702345E07332274
chr64670237046702461E07332434
chr64670249646703621E07332560
chr64670221046702345E07432274
chr64670237046702461E07432434
chr64670249646703621E07432560
chr64662211146622173E082-47763
chr64670221046702345E08232274
chr64670237046702461E08232434
chr64670249646703621E08232560