LD–Gene Region 1*.

*Change in simulated LD from original HapMap sample LD for each pair of SNPs in Gene Region 1 (LDsimulated – LDHapMap).**Sum of SNP pairs over all 100 replicates. The number of SNP pairs for Hapgen is not divisible by 100 because monoallelic SNPs were dropped from the LD calculations. Because Hapgen had more variation in MAF, it was more likely that a SNP with a low MAF would become monoallelic in one or more simulation replicates and would thus be dropped from the LD calculations.