Open Targets Genetics new release — version 3 — is out

Release Notes Jun 17, 2019

Breaking news directly from ESHG in Gothenburg!

We have a new release of Open Targets Genetics.

These are some of the highlights:

  • Colocalisation analysis

  • New molecular QTL datasets

  • Summary statistics from GWAS Catalog, SAIGE and UK Biobank Neale Round 2

  • More studies from GWAS Catalog and traits from UK Biobank

Colocalisation analysis

How can we try to make sense of the vast amount of association data between common genetic variants (e.g. SNPs from GWAS) and complex traits (e.g. chronic kidney disease) available out there? Can we identify the likely causal gene behind an association? Can we modulate this causal gene and possibly guide drug target identification?

We are a step closer towards answering these questions. For the first time, we now include statistical colocalisation analysis in Open Targets Genetics.

Colocalisation tests whether two independent association signals at a locus are consistent with having a shared causal variant. These are the two hypotheses we currently test:

  • H3: trait 1 and trait 2 have an independent association
  • H4 : trait 1 and trait 2 have a shared association

The comparison above can be either between a disease and a molecular trait or among diseases


Open Targets Genetics provides credible sets for studies, such as inflammatory bowel disease (de Lange KM, 2017), where summary statistics are used for colocalisation analysis

Check our new animation, Open Targets Genetics new colocalisation analysis, for a demo on how to explore this new data.

New molecular QTL datasets

We are working with Daniel Zerbino and his team at EMBL-EBI on a brand new Open Targets-EBI eQTL database, yet to go live.

However we have an early access to this resource, containing eQTL from a variety of cells, such as:

Cell type Consortium
Macrophage naive ALASOO
monocyte, neutrophil, T cells BLUEPRINT
Skin, fat, LCL TWINSUK
iPSC, neuron, etc many more

Summary statistics from GWAS Catalog and SAIGE

Over the last two years, GWAS Catalog has been hosting full p-value summary statistics for curated publications, if available from authors.

In addition to the p-value, summary statitics include odds ratio, beta coefficient, and confidence intervals, to name a few. Head to the supplementary data of the latest NHGRI-EBI GWAS Catalog paper, for the complete format of GWAS summary statistics.

In this new release, we are excited to announce that in addition to the 2,139 UK Biobank Neale round 2 sumstats, we have now incremented our fine mapping expansion analysis to provide a credible set of variants for:


Which studies have summary statistics? Search for any trait or study in Open Targets Genetics and find out.

More studies from GWAS Catalog

We have updated the GWAS Catalog traits to include their latest set of studies and traits, such as


Go to Open Targets Genetics to find all independently associated with carpal tunnel syndrome (p-value < 5e-8) and the top-ranked genes when assigning variants to genes


Are you at ESHG but missed From genetics to new medicines: the Open Targets Genetics Portal on Saturday?

Not to worry, the Open Targets Genetics team are still in Gothenburg and you can catch them at poster sessions, coffee breaks or on Twitter.

Get in touch by email or explore the help pages for an overview of Open Targets Genetics, its release notes and much more.