To analyze each region, we thinned SNPs in the simulated HapMap to match the density and allele frequency spectrum of the Phase II HapMap [The International HapMap Consortium, 2007]. Using the thinned data, we selected a panel of 100 tag SNPs for each region that included the 90 tag SNPs with the largest number of proxies and 10 additional SNPs selected at random among the remaining tags. This approach resulted in panels that captured ~78% of the common variants (MAF>5%) in the simulated CEU HapMap, similar to the real life performance of the Illumina 317K SNP genotyping chip. Finally, we analyzed each of the simulated datasets using the selected marker panel and one of three analysis strategies: (a) single marker chi-squared association tests, (b) single and multi-marker association tests [Pe’er et al., 2006] as suggested by the PLINK [Purcell et al., 2007] program based on the simulated HapMap, or (c) tests using imputed allele counts for all the markers in the simulated HapMap. Results are summarized in Table IV. The first row in the table shows the significance thresholds used
