Our analysis provides: (i) stronger signals of association at established T2D loci than logistic regression-based methods applied to all cases combined; (ii) confirmation of previous findings of heterogeneity in genetic effects at TCF7L2 and FTO according to obesity sub-phenotype in the same samples [Timpson et al., 2009]; and (iii) evidence of a novel potential T2D association with variants flanking Cullin-associated and neddylation-dissociated protein 1 (CAND1) in obese cases only. Here, FTO is linked to obesity due to melanocortin 4 receptor deficiency.