After stratification by gender, we found that the T/C genotype in the IL6R gene (rs2229238) and the G/G genotype in the LEPR gene (rs1137100) were associated with an increased risk of obesity only in males (OR = 2.27, 95% CI = 1.40–3.70, p = 0.0003 and OR = 2.80, 95% CI = 1.27–6.17, p = 0.028, respectively), while the T/G genotype in the IL18 gene (rs1946518) was associated with an increased risk of obesity only in females (OR = 2.02, 95% CI = 1.07–3.83, p = 0.03). Here, IL6R is linked to obesity due to melanocortin 4 receptor deficiency.