Somatic mutations in isocitrate dehydrogenases 1 (IDH1) have been identified as putative drivers in gliomas, and have profound impact on the epigenome by inhibiting α-ketoglutarate-dependent dioxygenases, including Tet and histone demethylases. To understand the role of IDH mutations in tumorigenesis, we profiled the epigenomes of IDH mutant gliomas and neural progenitor cells (NPCs). Compared to NPCs, IDH mutant gliomas showed a global increase in DNA methylation enriched in CpG islands. Surprisingly, for promoter hypermethylated regions associated with differentially expressed genes, only 46% were down-regulated, enriched in Frizzled proteins in Wnt pathway. Among the promoter hypermethylated and upregulated genes, 22% were also associated with loss of H3K27me3, and 21% with gain of H3K27ac. These genes were enriched in neurogenesis, including key transcription factors in neuronal differentiation such as LHX5. In addition, we found hypomethylation highly enriched in enhancers. These enhancers were enriched for binding sites of neuronal differentiation regulators, such as ASCL1 and OLIG2, both were up-regulated in IDH mutant gliomas and activated genes that promotes cell proliferation.