HelmholtzZentrum munich
WCMC

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

ONLINE SUPPLEMENTARY INFORMATION

Ideogram
Proteome annotation
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

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