SNPs were annotated to genes based on dbSNP version 135 SNP locations and NCBI 37.3 gene definitions. For the main analyses only SNPs located between a gene’s transcription start and stop sites were annotated to that gene, yielding 13,172 protein-coding genes containing at least one SNP in the CD data. An additional annotation using a 10 kilobase window around each gene was made, yielding 16,970 genes, to determine the effect of using a window on relative performance. These two gene annotations were used for all analyses, to ensure that differences in default annotation settings did not cloud the comparison between tools. The 1,320 Canonical Pathways from the MSigDB database [16] were used for the gene-set analysis. The relatively large number of gene sets and the fact that the MSigDB Canonical Pathways are drawn from a number of different gene-set databases ensures a wide variety of gene sets, which should prevent the results from being too dependent on the choice of gene-set database.
