Recent genome-wide association studies have identified several single nucleotide 
polymorphisms (SNPs) associated with body mass index (BMI)/obesity. In this 
study, we aim to examine the associations of obesity related loci with risk of 
metabolic syndrome (MetS) in a children population from China. A total of 431 
children with MetS and 3046 controls were identified based on the modified 
ATPIII definition. 11 SNPs (FTO rs9939609, MC4R rs17782313, GNPDA2 rs10938397, 
BDNF rs6265, FAIM2 rs7138803, NPC1 rs1805081, SEC16B rs10913469, SH2B1 
rs4788102, PCSK1rs6235, KCTD15 rs29941, BAT2 rs2844479) were genotyped by TaqMan 
7900. Of 11 SNPs, GNPDA2 rs10938397, BDNF rs6265, and FAIM2 rs7138803 were 
nominally associated with risk of MetS (GNPDA2 rs10938397: odds ratio (OR)=1.21, 
95% confidence interval (CI)=1.04-1.40, P=0.016; BDNF rs6265: OR=1.19, 95% 
CI=1.03-1.39, P=0.021; FAIM2 rs7138803: OR=1.20, 95% CI=1.02-1.40, P=0.025); 
genetic risk score (GRS) was significantly associated with risk of MetS 
(OR=1.09, 95% CI=1.04-1.15, P=5.26×10(-4)). After further adjustment for BMI, 
none of SNPs were associated with risk of MetS (all P>0.05); the association 
between GRS and risk of MetS remained nominally (OR=1.02, 95%CI=0.96-1.08, 
P=0.557). However, after correction for multiple testing, only GRS was 
statistically associated with risk of MetS in the model without adjustment for 
BMI. The present study demonstrated that there were nominal associations of 
GNPDA2 rs10938397, BDNF rs6265, and FAIM2 rs7138803 with risk of MetS. The SNPs 
in combination have a significant effect on risk of MetS among Chinese children. 
These associations above were mediated by adiposity.