Consistently significant pathways.

To avoid that a pathway is only significant due to a small number of significant SNPs, we performed the multistage integrative pathway (MIP) analysis pipeline four times with different constraints. In the first MIP run, all SNPs are included. In the next three runs, only those having a p-value smaller than a threshold of 10−3, 10−4, and 10−5, respectively, are included. This table lists all pathways that had a p-value smaller than 0.05 during all four MIP runs. The complete results of each disease are shown in supplementary Tables S2, S3 and S4, and a more detailed overview of all four MIP runs which also includes a comparison to the literature is depicted in Table S5.