We also imputed SNPs from 1000 Genomes Project pilot 1 calls obtained from Sanger Institute (August 12, 2009) based on 112 chromosomes from the HapMap CEU samples. This call set of SNPs contains 8,221,074 SNPs, and 6,625,013 of them have MAF > 5% in the imputed sample. In both the HapMap SNP and 1000 Genomes SNP imputation, we excluded SNPs with MACH R-square <0.3 from downstream analysis.
