We have designed Open Targets Genetics to be scalable and readily extensible. New data sources will continually be curated, reviewed, incorporated, and documented here and in the release notes. Please get in touch with any suggestions.
​GnomAD v2.1​
​1000 Genomes Phase 3 - used for LD expansion
​UK Biobank genotypes - used for conditional analysis in top-loci detection, fine-mapping and colocalisation analyses (approved application).
In silico functional prediction
​Variant-Effect Predictor (VEP): Most severe transcript consequence(s)
Molecular quantitative trait locus (QTL) experiments
​pQTL (Sun et al., 2018): Evidence linking genetic variation to protein abundance in Sun et al. (2018) pQTL data
eQTL: Evidence linking genetic variation to gene expression. See table below:
Consortium | Tissues/cell types |
​GTEX v7​ | 44 tissues |
ALASOO | Macrophage naive/IFNG/IFNG Salmonella |
BLUEPRINT | Monocyte, neutrophil, T cells |
CEDAR | B cells, Ileum, monocyte, neutrophil, platelet, rectrum, traverse colon, T cell CD4/CD8 |
FAIRFAX | Monocyte naive/IFN24/LPS2/LPS24, neutrophil, T cells, B cells |
GENCORD | Fibroblast, LCL, T cells |
GEUVADIS | LCL |
HIPSCI | iPSC |
NARANBHAI | Neutrophil CD16 |
NEDELEC | Macrophage naive/Listeria/Salmonella |
QUACH | Monocyte IAV/LPS/naive/PAM3CSK4/R848 |
SCHWAYZENTRUBER_2018 | Sensory neuron |
TWINSUK | Skin, fat, LCL |
VAN_DE_BUNT_2015 | Pancreatic islet |
eQTLGen | Blood |
Interaction / interval based experiments
​Promoter Capture Hi-C (Javierre et al., 2016): Evidence linking genetic variation to genes using Promoter Capture Hi-C in each of the 17 human primary hematopoietic cell types
​Enhancer-TSS correlation (Andersson et al., 2014): Evidence linking genetic variation to genes using correlation between the transcriptional activity of enhancers and transcription start sites using the FANTOM5 CAGE expression atlas
​DHS-promoter correlation (Thurman et al., 2012): Evidence linking genetic variation to genes using correlation of DNase I hypersensitive site and gene promoters across 125 cell and tissue types from ENCODE
Further details on each V2G dataset, including workflows to reproduce them, are located here.