CNV370 beadchip has only one-sixth of markers overlapping with Human1M beadchip. To know if the risk markers identified in AAs and EAs (Human1M) could be replicated in Australians (CNV370), we imputed the genotype data in Australians to fill in the missing markers and then performed association tests. First, we pre-phased the original genotype data 5 Mb around the risk genes of interest in Australians. Second, we used 1,000 Genome Project and HapMap 3 CEU datasets as reference panels to impute the missing genotypes in this 5 Mb region by the program IMPUTE2 [10]. This program uses a Markov Chain Monte Carlo (MCMC) algorithm to derive full posterior probabilities of genotypes of each SNP (burnin = 10, iteration = 30, k = 80 and Ne = 11,500). If the probability of one of the three genotypes of a SNP was over the threshold of 0.95, the genotypes of this SNP were then expressed as a corresponding allele pair for the following association analysis; otherwise, they were treated as missing genotypes. For SNPs that were directly genotyped, we used the direct genotypes
