In the replication study, the Fisher’s exact test or linear regression analysis showed association of rs9491140 in NKAIN2 with BMI in men (P = 0.036), rs145848316 in KMT2C with BMI in men (P = 0.030) and women (P = 0.010–0.019), and rs7863248 in AGTPBP1 with BMI in all individuals (P = 0.003–0.026) and men (P = 0.020–0.041) and with the prevalence of obesity (P = 0.016–0.049). Here, AGTPBP1 is linked to obesity due to melanocortin 4 receptor deficiency.