Imputation of genotypes from ERF and Rotterdam study was performed using Maximum Likelihood Method as implemented in the MACH software v 1.0.16. Release 22 HAPMAP CEU population was used as reference. This effort yielded a total of 2,500,000 SNPs. Only SNPs with call rates > 98%, MAF>1% and HWE P-values > 1e-06 were used for imputations. Mean r2 after imputations was 0.97 for the 19 SNPs tested within the 450 kb region on 12q21.31. For the MARS replication sample, the genotypes of rs1031681 were imputed using Impute v2.1.0 and the HapMap CEU as a reference population. rs1545843 failed QC in the controls of the UK sample with call rates < 98% and a p-value for differential missingness < 1e-08. Its genotypes were therefore imputed in both cases and controls using BEAGLE 3.1(Browning and Browning, 2009) on HapMap 3.
