The analysis was restricted to GO categories and KEGG pathways containing at least three genes, resulting in a total of 7652 gene sets. SNPs that mapped to within 20kb of a gene (genome build 36_3) were assigned to that gene, in order to include promoter and regulatory regions. If SNPs mapped within 20kb of more than one gene all such genes were included. The choice of a 20kb window is not entirely arbitrary, since a recent study of gene expression found that the majority of eQTLs lie within genes (Veyrieras et al. 2008). Any one SNP was not allowed to add more than one gene to any GO category, to prevent the analysis being biased by SNPs located in multiple functionally related overlapping genes. Gene sets required at least two signals to be counted as enriched, in order to remove the possibility of a small gene set being deemed significantly enriched based on one signal.
