Among the four genes with a significant TWMR effect (p ≤ 0.05/9 = 5.6 × 10−3), only SH2B1 had a directionally concordant effect (α = −0.23; p = 8.1 × 10−6) with the one observed in our CNV association study, i.e., increased SH2B1 expression decreased T2D risk, which is compatible with the deletion reducing the gene’s expression and increasing T2D risk. The gene discussed is SH2B1; the disease is type 2 diabetes mellitus.