Twenty-four CpGs were at/near obesity-related genes including three of the six novel BMI-associated CpGs, namely cg02871985 near THADA, cg08010984 in TNIK, and cg15103625 in RSRC1. cg08010984 in TNIK was inversely associated with BMI (P-value = 4.26 × 10–6) and the association was predominantly driven by Chinese (βChinese = − 27.24, βMalay = − 19.62, βIndian = − 18.96, PChinese = 2.14 × 10–7, PMalay = 0.23, PIndian = 0.16). This evidence concerns the gene TNIK and obesity due to melanocortin 4 receptor deficiency.