In summary, in our sample of Mexican children, we replicated four European obesity-related genes (GNPDA2, and nominally, NEGR1, MC4R and ENPP1) in the same direction of effect as previous findings, except for ENPP1. Interestingly, we found two novel association signals: between NPC1 variant and fasting serum insulin levels, and between MC4R variant and fasting plasma glucose levels. Here, NEGR1 is linked to obesity due to melanocortin 4 receptor deficiency.