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WCMC

Connecting genetic risk to disease endpoints through the human blood plasma proteome

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Locus annotations

Locus 140

Top associations per target

Target cis/​trans Study SNP SNP location Maj/​min allele MAF N βinv seinv Pinv fclog Plog Praw
PDK1 cis Discovery rs12052479 2:173,404,804 C/A 0.21 991 -0.572 0.050 2.5×10-28 -1.200 1.1×10-18 2.2×10-5
PDK1 cis Replication rs7596665 2:173,363,917 A/C 0.22 337 -0.226 0.077 0.004 -1.130 0.006 0.038

 

Regional association plots

[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 1, mitochondrial (PDK1)

Download the association data used to generate this plot

 

Boxplots and histograms for top associations

[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 1, mitochondrial (PDK1)

inverse-normalized probe levels log2 transformed probe levels raw probe levels
Discovery study
Replication study

[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 1, mitochondrial (PDK1)

Target (abbrv.) PDK1
Target (full name) [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 1, mitochondrial
Somalogic ID (Sequence ID) SL006921 (5227-60_3)
Entrez Gene Symbol PDK1
UniProt ID Q15118
UniProt Comment
  • Kinase that plays a key role in regulation of glucose and fatty acid metabolism and homeostasis via phosphorylation of the pyruvate dehydrogenase subunits PDHA1 and PDHA2. This inhibits pyruvate dehydrogenase activity, and thereby regulates metabolite flux through the tricarboxylic acid cycle, down-regulates aerobic respiration and inhibits the formation of acetyl-coenzyme A from pyruvate. Plays an important role in cellular responses to hypoxia and is important for cell proliferation under hypoxia. Protects cells against apoptosis in response to hypoxia and oxidative stress.
Targeted by drugs (based on IPA annotation)
  • dichloroacetic acid
Wiki Pathways
  • DNA damage response (only ATM dependent)
  • EPO Receptor Signaling
  • ErbB signaling pathway
  • TCA Cycle
  • TGF beta Signaling Pathway
Reactome
  • Regulation of pyruvate dehydrogenase (PDH) complex
  • Signaling by Retinoic Acid

All locus annotations are based on the sentinel SNP (rs12052479) and 17 proxy variant(s) that is/are in linkage disequilibrium r2 ≥ 0.8. Linkage disequilibrium is based on data from the 1000 Genomes Project, phase 3 version 5, European population and was retrieved using SNiPA's Block Annotation feature.
Download the detailed results of SNiPA's block annotation (PDF)

Linked genes

Genes hit or close-by
Potentially regulated genes
  • METAP1D methionyl aminopeptidase type 1D (mitochondrial)
  • PDK1 pyruvate dehydrogenase kinase, isozyme 1
eQTL genes
  • PDK1 pyruvate dehydrogenase kinase, isozyme 1

 

Results from other genome-wide association studies

Trait P Study Source
cg16060330 (chr2:173369180) 1.8×10-63 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
cg25053018 (chr2:173478019) 8.6×10-12 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
Serum ratio of (1-methylurate)/(1,7-dimethylurate) 1.7×10-5 21886157 (PMID) GRASP2 metabQTL
Alzheimer's disease (APOE4/E3 heterozygotes) 7.9×10-5 21379329 (PMID) GRASP2 nonQTL
Gene expression of PDK1 [probeset 226452_at] in sputum 9.1×10-5 21949713 (PMID) GRASP2 eQTL