To further explore additional signals not reaching genome-wide significance, we additionally performed a gene-based analyses – under the hypothesis that a given gene or genic region may harbor multiple susceptibility variants with p-values larger than the traditional GWAS significance level – with VEGAS, and a SNP and text-mining based analyses – identifying and prioritizing genes based on functional relationships identified using literature – with GRAIL. The top genes from the VEGAS analysis, using a Bonferroni correction for 17,640 genes, included previously implicated loci (FAM13A; CHRNB4, IREB2, CHRNA3/5, HYKK, and PSMA4 at 15q25); as well as RIN3 andAPOBR (Table S9). For the GRAIL analysis (Table S10), the top individual genes were OSM and OSMR; in contrast, genes at or near well-validated loci – HHIP, IREB2, andFAM13A – did not give significant P-values in the GRAIL analysis.
