RefSeq database83) and another time with putative regulatory regions taken into account using the same upstream/downstream windows as in the MAGMA analyses. Additionally, all SNPs not directly covered by our gene sets of interest were explicitly included into other annotations (‘non-genic’, ‘genic but not LoF intolerant’) on the basis of their genomic location. Finally, the ‘baseline’ set of 53 annotations from Finucane et al.26, which recapitulates important molecular properties such as presence of enhancers or phylogenetic conservation, was also incorporated in the model. All of these annotations were then tested jointly for heritability enrichment. We note that using exact genic coordinates or adding regulatory regions made little difference to the estimated enrichment of our gene sets; thus, throughout the manuscript, we report the latter for consistency with the gene set analyses (Fig. 2 and Supplementary Table 8).
