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WCMC

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

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Locus annotations

Locus 153

Top associations per target

Target cis/​trans Study SNP SNP location Maj/​min allele MAF N βinv seinv Pinv fclog Plog Praw
Semaphorin 3E cis Discovery rs536299 7:83,267,983 C/A 0.33 995 0.473 0.043 2.2×10-26 1.220 4.9×10-23 2.4×10-6
Semaphorin 3E cis Replication rs536299 7:83,267,983 C/A 0.20 337 0.400 0.087 5.6×10-6 1.170 1.6×10-4 0.519

 

Regional association plots

 

Boxplots and histograms for top associations

Semaphorin-3E (Semaphorin 3E)

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

Semaphorin-3E (Semaphorin 3E)

Target (abbrv.) Semaphorin 3E
Target (full name) Semaphorin-3E
Somalogic ID (Sequence ID) SL010470 (5363-51_3)
Entrez Gene Symbol SEMA3E
UniProt ID O15041
UniProt Comment
  • Plays an important role in signaling via the cell surface receptor PLXND1. Mediates reorganization of the actin cytoskeleton, leading to the retraction of cell projections. Promotes focal adhesion disassembly and inhibits adhesion of endothelial cells to the extracellular matrix. Regulates angiogenesis, both during embryogenesis and after birth. Can down-regulate sprouting angiogenesis. Required for normal vascular patterning during embryogenesis. Plays an important role in ensuring the specificity of synapse formation (By similarity).
Pathway Interaction Database
  • Plexin-D1 Signaling
Reactome
  • Other semaphorin interactions

All locus annotations are based on the sentinel SNP (rs536299) and 23 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
  • SEMA3E sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E
eQTL genes
  • SEMA3E sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E

 

Results from other genome-wide association studies

Trait P Study Source
cg18464137 (chr7:83278480) 6.8×10-19 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
cg05855618 (chr7:83277941) 3.1×10-14 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
cg19542238 (chr7:83278114) 5×10-10 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
cg02572463 (chr7:83277917) 4.9×10-8 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
cg08274234 (chr7:83277995) 3.5×10-7 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
cg23889875 (chr7:83278090) 8.7×10-5 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
1-eicosadienoylglycerophosphocholine* 9.3×10-5 24816252 (PMID) gwas.eu via SNiPA
Autism with low IQ 1.8×10-4 20663923 (PMID) GRASP2 nonQTL
Waist circumfence 4.1×10-4 25673412 (PMID) Supplemental file