Imputation for the SAGE data was performed using BEAGLE version 3.3.1, (Browning and Browning 2007) for all autosomes and the X chromosome, with the December 2010 released genotypes and haplotype reference panels selected from the 1000 Genomes Project (www.1000genomes.org). EUR analysis panel was used to impute the EA samples. In SAGE we did not have the advantage of family based cleaning; therefore, we based our analysis on 4,058,415 common SNPs that met imputation quality control criteria across both SAGE and COGA datasets.
