OmniExpress and 668,283 SNPs for Affymetrix 6.0. However, the intersection among all three platform families was only 75,285 SNPs (Fig 1). To achieve the largest GWAS datasets as possible without losing SNP information, we created three datasets–HumanHap comprising six GWAS datasets, OmniExpress comprising four GWAS datasets and Affymetrix 6.0 comprising two GWAS datasets. In the merging process, we removed any SNPs that were not in all studies for a specific platform or had a missing call rate>5%. We flipped strands where appropriate and removed A/T and C/G SNPs to create the final compiled datasets.
