To determine likely causal genes at each locus, we used a combination of criteria. The gene nearest to each top SNP was selected by default. This gene was replaced or added to if the top SNP was (in high LD with) an expression quantitative-trait locus (eQTL) or a non-synonymous variant in another gene, or if there was an alternative neighbouring biological candidate gene. 31/123 signals mapped as eQTLs in data from Westra et al. (E)10, five were annotated as non-synonymous functional (F), 60 as biological candidates (C), and four mapped to gene deserts (nearest gene >500 kb) (Supplementary Tables 6-8). We also used publicly available whole blood and adipose tissue methylation-QTL data to map 9/123 signals to cis-acting changes in methylation level (Extended Data Table 5)9.
