For each SNP in Table 2, we assessed the additive SNP association in the stage 1 and 2 samples before and after including body mass index in the logistic regression model. For each genotyped and imputed SNP surrounding a specific T2D signal we assessed the additive SNP association in the stage 1 sample before and after including the Table 2 SNP from the same region in the model. We analyzed the data and adjusted for covariates for the stage 1 and stage 2 analysis of each sample. Data were combined across studies as described above. The ORs and CIs were calculated using a fixed-effects model and p values were calculated using the weighted z-score method. For the UK stage 1 samples, we did not have BMI information available for ~1,500 of the population-based controls. We therefore carried out the conditional BMI analyses by using all T2D cases and only those controls for whom BMI data were available.
