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 changelog. Please get in touch with any suggestions.

Variant index

Disease-associated loci sources (V2D)

Haplotype reference samples

Variant-to-Gene annotation sources (V2G)

  • In silico functional prediction

  • Molecular quantitative trait locus (QTL) experiments

    • eQTL: Evidence linking genetic varition to gene expression (see table below)

    • pQTL (Sun et al., 2018): Evidence linking genetic varition to protein abundance in Sun et al. (2018) pQTL data

  • Interaction / interval based experiments

Further details on each V2G dataset, including workflows to reproduce them, are located here.

eQTL datasets

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