Enhancers are crucial regulators of gene transcription, and their aberrations have been implicated in the dysregulation of genes in cancer. However, existing studies primarily focus on genetic alterations around enhancers in cancer. The effect of enhancer shifts in the 3D genome on gene expression remains unclear. In this study, we identify all the reversed expression of gene pairs targeted by the enhancers from 9,697 tumor samples and 8,284 normal samples in 28 cancer types. By examining the chromosome conformation near these gene pairs, we find that the shift of potential oncogenic enhancers in the 3D genome, from one target gene to the other, may significantly induce the reversed expression of this target gene pair in cancer. Specifically, one target gene of the enhancer exhibits higher expression than the other one in normal samples, whereas it switches to lower expression in cancer. Furthermore, we develop a database, EnShiftDB (http://www.easonlcheng.cn/EnShiftDB/), to display the information regarding enhancer shifts in the 3D genome and the corresponding reversed target gene pairs in 28 cancer types. Our study offers an epigenetic perspective on gene dysregulation in carcinogenesis and facilitates the further exploration of enhancers in carcinogenesis.