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Data Sources

This section contains information about the data source harmonisation tools available in Open Targets Gentropy.

GWAS study sources

  1. GWAS Catalog (with or without full summary statistics)
  2. FinnGen
  3. FinnGen UK Biobank and Million Veteran Program (MVP) meta-analysis

Molecular QTLs

  1. GTEx (eQTL catalogue)
  2. UKB PPP (EUR)
  3. deCODE proteomics

Protein complexes

  1. Complex Portal

Interaction / Interval-based Experiments

  1. Intervals-based datasets, informing about the relationships between genetic elements and their functional implications.

Variant annotation/validation

  1. GnomAD v4.1
  2. GWAS catalog's harmonisation pipeline
  3. Ensembl's Variant Effect Predictor

Linkage disequilibrium

  1. GnomAD v2.1.1 LD matrixes (7 ancestries)

Locus-to-gene gold standard

  1. Open Targets training set

Gene annotation

  1. Open Targets Platform Target Dataset (derived from Ensembl)

Biological samples

  1. Uberon and Cell Ontology