Data Sources

 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.  
Variant index
​GnomAD v2.1​
Disease-associated loci sources (V2D)
​GWAS Catalog curated studies​
​GWAS Catalog summary statistics​
​Neale lab UK Biobank summary statistics​
​SAIGE UK Biobank summary statistics​
​FinnGen summary statistics​
Haplotype reference samples
​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).
Variant-to-Gene (V2G) annotation sources
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.

Our Approach - Previous

Colocalisation analysis

Next - Our Approach

FinnGen

Last modified 5mo ago

Copy link