HelmholtzZentrum munich

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


Proteome annotation
pGWAS server

Welcome to the pGWAS server

This website supplements our publication "Connecting genetic risk to disease endpoints through the human blood plasma proteome".
In our study, we performed a genome-wide association study with protein levels (pGWAS). Using a highly multiplexed, aptamer-based, affinity proteomics platform (SOMAscan™), we quantified levels of 1,124 proteins in blood plasma samples from 1,000 German individuals (KORA cohort) and 338 Arab or Asian individuals (QMDiab cohort).
We identified 539 independent, genome-wide significant SNP-to-protein associations, which can be investigated using this webserver.

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How to cite

The manuscript accompanying this website was published in Nature Communications:
Suhre K et al., Connecting genetic risk to disease endpoints through the human blood plasma proteome. Nature Communications (2017); doi:10.1038/ncomms14357

A preprint (not peer-reviewed) version of the manuscript is available at bioRxiv (doi:10.1101/086793)


This website is a joint project of the Institute of Bioinformatics and Systems Biology (IBIS) at the Helmholtz Zentrum M√ľnchen and the Bioinformatics Core Facility at the Weill Cornell Medical College in Qatar.
It was developed and is being maintained by Matthias Arnold and Johannes Raffler, both members of the IBIS Metabolomics group.

Please feel free to contact us if you have any questions regarding the contents of this site.


  • Dec 09, 2019: added list of probe annotations to download section
  • Jun 28, 2018: added probe annotations for pGWAS hits reported in Sun et al. (Nature, 2018)
  • May 28, 2018: added link to GDPR policy
  • May 22, 2017: fixed issues with occasionally flipped effect alleles for (imputed) sentinel variants in files used for regional association plots
  • May 22, 2017: added missing plots to Supplemental Figure 6 ZIP archives
  • Feb 28, 2017: added full associations results file to the download section
  • Feb 27, 2017: link to final manuscript in Nature Communications
  • Feb 13, 2017: updates for loci #98 and #259 regarding Complement C1s subcomponent as well as for locus #157 regarding Alkaline phosphatase
  • Nov 16, 2016: minor bug fixes, including URL to NCI's Pathway Interaction Database
  • Nov 09, 2016: unrestricted access following the preprint release of the manuscript
  • Apr 27, 2016: initial release, accessible for reviewers only