Conclusions: There is a linkage imbalance between rs9939609 and rs17817449 in a Central China general population cohort, which also reflected the influence of FTO gene on the risk of overweight/obesity and total cholesterol (TC), triglyceride (TG), and high-density lipoprotein (HDL) disorders. Here, FTO is linked to obesity due to melanocortin 4 receptor deficiency.