Quality control (QC) criteria for SNPs to be included in the meta-analysis were minor allele frequency (MAF)≥1% and for imputed SNPs good imputation quality, which was defined as proper_info≥0.4 (for studies analysed with IMPUTE) or rsq-hat≥0.3 (for studies analysed using MACH). The rsq_hat measure allows us to assess imputation accuracy for markers with many different allele frequencies. In comparison to filters based on the accuracy of individual genotype calls, it generally translates into a more stringent standard for rare SNPs and a more lenient standard for common SNPs. For intuition on how the measure performs consider the simple example of region where a particular SNP always occurs in a specific haplotype background. Further, assume that the SNP has a frequency of 10% and that the haplotype has a frequency of 20%. In this example, whenever we observed this particular haplotype we expect the SNP will be present ∼50% of the time so that >50% imputation accuracy cannot be achieved for this SNP. On the other hand, knowledge of the haplotype does provide useful information about the SNP, and the rsq_hat
