We removed SNPs with HWE p < 0.0001 (in controls) or call rates < 95% or minor allele frequency (MAF) <1% leaving 778,974 SNPs for the COGA sample and 818,773 SNPs for the SAGE sample for further analysis. P-values from the Cochranes’s Q values were provided for evaluating and testing the heterogeneity of variance in the effect sizes of selected studies.
