Our genome-wide results for the trend test are illustrated in Fig. 4. The single-disease trend and genotypic tests for SNPs on the chip identified 21 signals across the 7 diseases that exceeded a threshold of 5×10-7 (Table 3). For each of these SNPs (except those within the MHC), cluster plots are shown in Supplementary Fig. 10 and ‘signal plots’ in Fig. 5. These signal plots estimate the likely demarcation of the hit region and show the signal at genotyped and imputed SNPs together with local genomic context. Four further strong (with P<5×10-7) associations were revealed by the other primary analyses described (Table 3). One locus (in RA) was revealed by the sex-differentiated analysis, two through multilocus approaches (both for T1D) and one through an analysis which combined cases from more than one autoimmune disease (signal plots in Supplementary Figs 11, 12 and 13, respectively).
