poor; these resided in the proximity of 35 of the significant SNPs. We subsequently removed these SNPs and re-imputed. We found that following post-imputation QC filtering, only 3 of the 61 SNPs were no longer significant, and the R2 remained the same as for the QCed data (R2=0.994) for the post-imputation QC filtered data. When we repeated comparisons using IMPUTE v2 with the HapMap3 (CEU, release no. 2 February 2009) and data from the 1000 genomes project (Pilot 1 genotypes released March 2010; phased haplotypes released June 2010) as the reference panels, we observed qualitatively similar results.
