Using the additive model, six SNPs revealed significant associations with obesity after multiple testing correction (Bonferroni corrected P < 0.004), with odds ratios (ORs) from 1.211 to 1.421, namely FTO-rs1558902 (P = 5.6×10−5), MC4R-rs2331841 (P = 4.4×10−4), GNPDA2-rs16858082(P = 3.4×10−4), PCSK1-rs261967 (P = 0.001), SEC16B-rs516636 (P = 0.004), and MAP2K5-rs4776970 (P = 0.004), while other two loci, ITIH4-rs2535633 (P = 0.012) and BDNF-rs2030323(P = 0.031), showed nominal association with obesity, with ORs 1.157 and 1.133, respectively. Here, GNPDA2 is linked to obesity due to melanocortin 4 receptor deficiency.