After adjusting the association of each SNP, the genomic control inflation parameter was 1.016 compared with 1.024 in the unadjusted analysis. Of the four reported associations with prognosis, three of the lead SNPs remained genome-wide significant, while association of the lead SNP in the MHC region was attenuated to just short of genome-wide significance. However, another MHC SNP, which was genome-wide significant in the index study, did remain so after adjustment (Table 5). Following Lee et al.6, we inspected the associations with prognosis of 170 SNPs robustly associated with incidence (Supplementary Data 1). None of these SNPs were significantly associated with prognosis, after correcting for 170 tests.Table 5P-values for four regions associated with Crohn’s disease prognosisChromosomeMbVariantNearest geneUnadjusted PAdjusted PX112.9rs5929166 XACT 4.56e-96.56e-9631.7rs9279411 MHC 5.46e-97.93e-8631.7rs114575504 MHC 9.37e-94.46e-86109.0rs3778586 FOX03 1.47e-82.66e-8745.9rs75764599 IGFBP1 4.32e-84.00e-8Unadjusted P, Wald test P-value reported by Lee et al.6. Adjusted P, Wald test P-value from our adjusted analysis. The lead variant in MHC in Lee et al., rs9279411 does not achieve genome-wide significance in our adjusted analysis but is ~72 kb proximal to rs114575504, which does achieve significance
