Abstract: Relationship between single nucleotide polymorphism on FTO gene rs9939609 and obesity in children　WU Yanming, LI Weiguo, SHENG Qiuming, DAI Jinsheng, ZHANG Lingjun, WU Min, GONG Huijun (Department of Pediatrics, Shanghai Pudong New Area People’s Hospital, Shanghai 201200, China)#br#Objective To investigate the relationship of single nucleotide polymorphism (SNP) on FTO gene rs9939609 with metabolism index and obesity in children. Methods One hundred and fifty-three children (age 7-11 year) were recruited in this study, 102 of them were obese and 51 of them were overweight. One hundred and sixty children with normal body weight were recruited as control. Height, weight and biochemical indicator of liver function were measured. PCR and direct sequence were applied to detect the polymorphism of rs9939609, and the frequency of the allele was calculated. Results TT or TA/AA genotype frequency on FTO gene rs9939609 was significantly different among overweight group, obesity group and normal control group (χ²=23.01, P<0.001); TA/AA genotype frequency in overweight and obesity group was significant higher than that in the control group（P<0.014）. The frequencies of T and A allele in overweight group, obesity group and control group was 96.25% and 3.75%, 85.29% and 14.71%, 85.78% and 14.22% respectively. There was significant difference of allelic frequency among overweight group, obesity group and control group (χ²=21.72, P<0.001). The frequency of A allele in overweight and obesity group was higher than that in control group (P'<0.014). Subjects with TA/AA allele had significantly higher BMI compared with subjects with TT allele. Conclusions rs9939609 of FTO gene is associated with obesity in children, and allele A on this spot may raise BMI and leads to overweight and obesity.