distance = 2.4 Mb, r2 = 0.01 in HapMap). Excluding the MHC region, we identified six regions with at least one SNP associated at P < 10−5 and a second SNP with a conditionally independent P < 10−3 (Supplementary Table 5). We performed 100 simulations after permuting case-control status randomly within each study. In contrast to the six regions in the real dataset, we never observed more than a single region with co-localized statistically independent signals in any simulated genome-wide scan, indicating our observation is highly unlikely to have occurred by chance.
