Three out of the 23 sub-genome-wide lead variants lay in or near the known type 2 diabetes loci TACC2, FGFR2 and CCND2. We considered them as distinct variants as they retained locus-wide significance (p<5 × 10−5) after conditioning on the nearest known associated variant. Here, FGFR2 is linked to type 2 diabetes mellitus.