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WCMC

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

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Locus annotations

Locus 340

Top associations per target

Target cis/​trans Study SNP SNP location Maj/​min allele MAF N βinv seinv Pinv fclog Plog Praw
GPC5 cis Discovery rs2147190 13:92,058,888 C/T 0.34 993 0.334 0.045 2.3×10-13 1.120 7.2×10-11 0.589
GPC5 cis Replication rs7325533 13:92,047,229 C/A 0.29 337 0.171 0.081 0.035 1.060 0.058 0.109

 

Regional association plots

 

Boxplots and histograms for top associations

Glypican-5 (GPC5)

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

Glypican-5 (GPC5)

Target (abbrv.) GPC5
Target (full name) Glypican-5
Somalogic ID (Sequence ID) SL012469 (4991-12_1)
Entrez Gene Symbol GPC5
UniProt ID P78333
UniProt Comment
  • Cell surface proteoglycan that bears heparan sulfate.
Reactome
  • A tetrasaccharide linker sequence is required for GAG synthesis
  • Defective B3GAT3 causes JDSSDHD
  • Defective B4GALT7 causes EDS, progeroid type
  • Defective EXT1 causes exostoses 1, TRPS2 and CHDS
  • Defective EXT2 causes exostoses 2
  • HS-GAG biosynthesis
  • HS-GAG degradation
  • Release of Hh-Np from the secreting cell
  • Retinoid metabolism and transport

All locus annotations are based on the sentinel SNP (rs2147190) and 12 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
eQTL genes

 

Results from other genome-wide association studies

Trait P Study Source
cg20647118 (chr13:92051762) 9.4×10-102 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
cg26960333 (chr13:92051729) 2.3×10-63 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
cg22284043 (chr13:92051552) 1.7×10-58 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
Height 1.2×10-7 25282103 (PMID) Supplemental file
Rheumatoid arthritis, combined control dataset 2.4×10-4 17554300 (PMID) GRASP2 nonQTL
Parkinson's disease 4.4×10-4 22451204 (PMID) GRASP2 nonQTL