Of 11 studied SNPs, four SNPs and genetic risk score (GRS) based on them were statistically significantly associated with central obesity by WC criteria (FTO rs9939609: OR = 1.29, 95%CI = 1.10–1.50, p = 0.001; MC4R rs17782313: OR = 1.27, 95%CI = 1.12–1.44, p = 1.32×10−4; GNPDA2 rs10938397: OR = 1.22, 95%CI = 1.09–1.37, p = 4.09×10−4; BDNF rs6265: OR = 1.20, 95%CI = 1.08–1.34, p = 8.86×10−4; GRS: OR = 1.25, 95%CI 1.16–1.34, p = 2.58×10−9) after adjustment for sex, age, pubertal stage, physical activity and family history of obesity. Here, MC4R is linked to obesity due to melanocortin 4 receptor deficiency.