The case-control design is vulnerable to population stratification and admixture effects. To control for these effects, we also performed structured association analysis. First, we estimated the ancestry proportions for each unrelated subject, based on the information content of 37 AIMs using the program STRUCTURE (Pritchard et al 2000a). Parameters for burn-ins, iterations, and k were set as 100,000, 100,000 and 2, respectively. STRAT (Pritchard et al 2000b) was used to analyze allelewise and genotypewise associations between the candidate markers and CD by excluding the admixture effects. We performed 10,000 simulation iterations per marker.
