This file contains all differentially methylated regions (DMRs) that were identified between human embryonic stem cells (hESCs) and three in vitro derived populations from each germ layer mesoderm, endoderm and ectoderm using a 5 day differentiation protocol. In addition, we provide the methylation level of all regions in these four populations as well as in hESC derived neural precursor populations neuroepithelial (day 12), early radial glia (day 14) and mid radial glia (day 35). All coordinates are given for hg19, X and Y chromosomes were excluded from the analysis. Columns: DMR_Mesoderm, DMR_Endoderm, DMR_Ectoderm  indiciate in which germ layer each region was detected as a DMR. DMRs were defined as regions exhibiting significant (p<=0.01) methylation difference >=0.3 between two conditions. DMR identification was conducted as previously described (Ziller et al. 2014).