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From the article you posted:

We simulated three categories of candidate SNPs to compare the effectiveness of different stratification correction methods. For the first category (random SNPs with no association to disease), we again used the Balding-Nichols model with FST ¼ 0.01 (see Methods). For the second category (differentiated SNPs with no association), we assumed population allele frequencies of 0.80 for population 1 and 0.20 for population 2. This category was motivated by previous studies of a SNP in the lactase (LCT) gene, which was shown to be spuriously associated to the height phenotype in European Americans because of stratification6; this SNP varies in frequency from 0.20 to 0.80 in European populations because of positive selection28. For the third category (causal SNPs), we used the Balding-Nichols model with FST ¼ 0.01 and a multiplicative disease risk model with a relative risk of 1.5 for the causal allele (see Methods).