To the best of our knowledge, our study is the first to find that 1) the HIF3A rs3826795 polymorphism interacts with obesity on plasma ALT, with the rs3826795 G-allele number elevating the ALT level only in obese children; and 2) the effect of the HIF3A rs3826795 polymorphism on ALT in obese children is mediated by HIF3A DNA methylation. Here, HIF3A is linked to obesity disorder.