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

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Locus annotations

Locus 15

Top associations per target

Target cis/​trans Study SNP SNP location Maj/​min allele MAF N βinv seinv Pinv fclog Plog Praw
PDGF Rb cis Discovery rs3776081 5:149,532,107 T/C 0.32 995 -0.961 0.037 3.3×10-113 -1.580 1.5×10-115 8.7×10-20
PDGF Rb cis Replication rs3776081 5:149,532,107 A/G 0.44 337 -0.732 0.057 3.5×10-31 -1.500 1.2×10-32 2.4×10-32

 

Regional association plots

Platelet-derived growth factor receptor beta (PDGF Rb)

Download the association data used to generate this plot

 

Boxplots and histograms for top associations

Platelet-derived growth factor receptor beta (PDGF Rb)

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

Platelet-derived growth factor receptor beta (PDGF Rb)

Target (abbrv.) PDGF Rb
Target (full name) Platelet-derived growth factor receptor beta
Somalogic ID (Sequence ID) SL004155 (3459-49_2)
Entrez Gene Symbol PDGFRB
UniProt ID P09619
UniProt Comment
  • Tyrosine-protein kinase that acts as cell-surface receptor for homodimeric PDGFB and PDGFD and for heterodimers formed by PDGFA and PDGFB, and plays an essential role in the regulation of embryonic development, cell proliferation, survival, differentiation, chemotaxis and migration. Plays an essential role in blood vessel development by promoting proliferation, migration and recruitment of pericytes and smooth muscle cells to endothelial cells. Plays a role in the migration of vascular smooth muscle cells and the formation of neointima at vascular injury sites. Required for normal development of the cardiovascular system. Required for normal recruitment of pericytes (mesangial cells) in the kidney glomerulus, and for normal formation of a branched network of capillaries in kidney glomeruli. Promotes rearrangement of the actin cytoskeleton and the formation of membrane ruffles. Binding of its cognate ligands - homodimeric PDGFB, heterodimers formed by PDGFA and PDGFB or homodimeric PDGFD -leads to the activation of several signaling cascades; the response depends on the nature of the bound ligand and is modulated by the formation of heterodimers between PDGFRA and PDGFRB. Phosphorylates PLCG1, PIK3R1, PTPN11, RASA1/GAP, CBL, SHC1 and NCK1. Activation of PLCG1 leads to the production of the cellular signaling molecules diacylglycerol and inositol 1,4,5-trisphosphate, mobilization of cytosolic Ca(2+) and the activation of protein kinase C. Phosphorylation of PIK3R1, the regulatory subunit of phosphatidylinositol 3-kinase, leads to the activation of the AKT1 signaling pathway. Phosphorylation of SHC1, or of the C-terminus of PTPN11, creates a binding site for GRB2, resulting in the activation of HRAS, RAF1 and down-stream MAP kinases, including MAPK1/ERK2 and/or MAPK3/ERK1. Promotes phosphorylation and activation of SRC family kinases. Promotes phosphorylation of PDCD6IP/ALIX and STAM. Receptor signaling is down-regulated by protein phosphatases that dephosphorylate the receptor and its down-stream effectors, and by rapid internalization of the activated receptor.
Targeted by drugs (based on IPA annotation)
  • nilotinib
  • dasatinib
  • sunitinib
  • pazopanib
  • axitinib
  • tivozanib
  • tandutinib
  • nintedanib
  • regorafenib
  • bortezomib/sorafenib
  • lapatinib/pazopanib
  • dexamethasone/lenalidomide/sorafenib
  • bevacizumab/sorafenib
  • imatinib/sirolimus
  • imatinib
  • sorafenib
  • becaplermin
Biomarker applications (based on IPA annotation)
  • prognosis
  • response to therapy
  • unspecified application
Wiki Pathways
  • Focal Adhesion
  • MAPK signaling pathway
  • Osteoblast Signaling
  • Regulation of Actin Cytoskeleton
Pathway Interaction Database
  • Beta3 integrin cell surface interactions
  • Nectin adhesion pathway
  • PDGF receptor signaling network
  • PDGFR-beta signaling pathway
  • S1P1 pathway
  • S1P3 pathway
  • SHP2 signaling
  • Signaling events mediated by PTP1B
  • Signaling events mediated by TCPTP
  • Urokinase-type plasminogen activator (uPA) and uPAR-mediated signaling
  • Validated targets of C-MYC transcriptional repression
Reactome
  • Constitutive Signaling by Aberrant PI3K in Cancer
  • Downstream signal transduction
  • PIP3 activates AKT signaling
  • Signaling by PDGF
Pathway Studio
  • PDGFR → AP-1/MYC signaling
  • PDGFR → FOXO3A signaling
  • PDGFR → STAT signaling
  • UrokinaseR → ELK-SRF signaling

All locus annotations are based on the sentinel SNP (rs3776081) and 2 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


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Genes hit or close-by
  • PDGFRB platelet-derived growth factor receptor, beta polypeptide
eQTL genes
  • PDGFRB platelet-derived growth factor receptor, beta polypeptide
  • CDX1 caudal type homeobox 1
  • CSF1R colony stimulating factor 1 receptor

 

Results from other genome-wide association studies

Trait P Study Source
P09619 protein abundance levels 1.2×10-6 22595970 (PMID) GRASP2 pQTL
Gene expression of PDGFRB [probe ILMN_25767] in osteoblasts treated with dexamethasone 2.9×10-5 21283786 (PMID) GRASP2 eQTL
Gene expression of PDGFRB [probeset 202273_at] in sputum 3×10-4 21949713 (PMID) GRASP2 eQTL