The generated gene-based P-values were used to analyze sets of genes in order to test for enrichment of association signals in genes belonging to specific biological pathways or processes. In the analysis only genes on autosomes, and genes located outside the broad MHC region (hg19:chr6:25–35M) were included. We used the gene names and locations and the European genotype reference panel provided with MAGMA. For gene sets we used sets with 10–1000 genes from the Gene Ontology sets86 currated from MsigDB 6.087.
