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Background  Large-scale genome-wide association studies have identified multiple genetic variants that are associated with elevated body mass index (BMI) or the risk of obesity in Caucasian or Asian populations. We examined whether these variants are individually associated with obesity in Chinese children, and also assessed their cumulative effects and predictive value for obesity risk in Chinese children.    Methods  We genotyped 40 single nucleotide polymorphisms (SNPs) and conducted association analyses for 32/40 SNPs with an estimated minor allele frequency >1 % in 2 030 unrelated Chinese children, including 607 normal-weight, 718 overweight, and 705 obese individuals from two cross-sectional study groups. Logistic regression and linear regression under the additive model were used to examine associations, and the area under the receiver operating characteristic curve (AUC ROC ) was reported as prediction summary.    Results  We identified obesity association for 6 SNPs near  SEC16B, RBJ, CDKAL1, TFAP2B, MAP2K5  and  FTO  (odds ratios (ORs) ranged from 1.19 to 1.41, nominal two-sided  P -values < 0.05). Association (Bonferroni corrected) of rs543874 near  SEC16B  and rs2241423 near  MAP2K5  had presumably stronger effects on obesity in Chinese children than in Caucasian populations. Their risk alleles were also associated with BMI standard deviation score (BMI-SDS) variability. We demonstrated the cumulative effects of the 32 SNPs on obesity risk (per risk allele: OR = 1.06, 95 % CI: 1.03-1.11,  P  = 4.84 × 10 -4 ) and BMI-SDS (β = 0.04, 95 % CI: 0.02-0.06,  P  = 3.69 × 10 -7 ). The difference in AUC ROC  for a model with covariates (age, age square, sex and study group) and the model including covariates and all 32 SNPs was 2.8 % ( P  = 0.0002).    Conclusion  While six SNPs were individually associated with obesity in Chinese children, the 32 common variants identified by recent GWA studies had cumulative effects and resulted in a limited increase in the AUC ROC  predictive value for childhood obesity.    Electronic supplementary material  The online version of this article (doi:10.1186/s12881-016-0268-4) contains supplementary material, which is available to authorized users.

Association of common variants identified by recent genome-wide association studies with obesity in Chinese children: a case-control study