Data Sources

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:

• 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.