In order to implicate the likely causal gene (or genes) for each of the novel and previously-reported signals (97 in total), we employed functional annotation and analysis of gene expression data. All variants within 25kb, variants within 500kb and with r2>0.5 of the top SNP at each signal and variants within 1Mb and with r2>0.8 with the top SNP were annotated using ENSEMBL’s Variant Effect Predictor (VEP). A variant was labelled as deleterious if it was a missense coding variant that was annotated as ‘deleterious’ by SIFT, ‘probably damaging’ or ‘potentially damaging’ by PolyPhen-2, had a CADD scaled score ≥ 20 (CADD_PHRED ≥ 20), or had a GWAVA score > 0.5. The deleterious variants were each, in turn, included as a covariate in the association analysis for the top SNP. If inclusion of the deleterious variant as a covariate reduced the association signal for the top SNP such that P>0.01, that deleterious variant was deemed to explain part of the signal. If annotation (e.g. a coding variant) implicated a specific gene, then the gene was classified as a high-priority gene for the relevant signal.
