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WCMC

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

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Locus annotations

Locus 388

Top associations per target

Target cis/​trans Study SNP SNP location Maj/​min allele MAF N βinv seinv Pinv fclog Plog Praw
EPHB2 cis Discovery rs6687487 1:23,061,551 G/A 0.09 994 -0.529 0.075 3.5×10-12 -1.100 5.7×10-12 1.3×10-11
EPHB2 cis Replication rs61488959 1:23,066,767 A/C 0.10 337 -0.250 0.067 2.3×10-4 -1.080 0.001 0.001

 

Regional association plots

 

Boxplots and histograms for top associations

Ephrin type-B receptor 2 (EPHB2)

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

Ephrin type-B receptor 2 (EPHB2)

Target (abbrv.) EPHB2
Target (full name) Ephrin type-B receptor 2
Somalogic ID (Sequence ID) SL007179 (5077-28_3)
Entrez Gene Symbol EPHB2
UniProt ID P29323
UniProt Comment
  • Receptor tyrosine kinase which binds promiscuously transmembrane ephrin-B family ligands residing on adjacent cells, leading to contact-dependent bidirectional signaling into neighboring cells. The signaling pathway downstream of the receptor is referred to as forward signaling while the signaling pathway downstream of the ephrin ligand is referred to as reverse signaling. Functions in axon guidance during development. Involved in the guidance of commissural axons, that form a major interhemispheric connection between the 2 temporal lobes of the cerebral cortex. Also involved in guidance of contralateral inner ear efferent growth cones at the midline and of retinal ganglion cell axons to the optic disk. In addition to axon guidance, also regulates dendritic spines development and maturation and stimulates the formation of excitatory synapses. Upon activation by EFNB1, abolishes the ARHGEF15-mediated negative regulation on excitatory synapse formation. Controls other aspects of development including angiogenesis, palate development and in inner ear development through regulation of endolymph production. Forward and reverse signaling through the EFNB2/EPHB2 complex regulate movement and adhesion of cells that tubularize the urethra and septate the cloaca. May function as a tumor suppressor.
Biomarker applications (based on IPA annotation)
  • unspecified application
Wiki Pathways
  • Keap1-Nrf2 Pathway
  • NLR proteins
Pathway Interaction Database
  • EPHB forward signaling
  • Ephrin B reverse signaling
  • EphrinB-EPHB pathway
  • Syndecan-2-mediated signaling events
Reactome
  • EPH-Ephrin signaling
  • EPH-ephrin mediated repulsion of cells
  • EPHB-mediated forward signaling
  • Ephrin signaling
  • L1CAM interactions
Pathway Studio
  • EPHB → NMDA receptor activation
  • EphrinB → JUN signaling

All locus annotations are based on the sentinel SNP (rs6687487) and 4 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
  • C1QA complement component 1, q subcomponent, A chain
  • C1QA
  • C1QB complement component 1, q subcomponent, B chain
  • C1QB
eQTL genes

 

Results from other genome-wide association studies

Trait P Study Source
cg00323313 (chr1:23054939) 3.8×10-65 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
Gene expression of EPHB2 in peripheral blood monocytes 4.7×10-20 20502693 (PMID) GRASP2 eQTL
cg20149170 (chr1:23105124) 1×10-7 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
cg08264906 (chr1:23197204) 6.4×10-5 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
Agreeableness 2.7×10-4 21173776 (PMID) Supplemental file
Fasting blood glucose 4.2×10-4 20081858 (PMID) GRASP2 nonQTL