We propose a novel method for reconstructing the whole-genome chromatin ensemble from the Hi-C data. The procedure starts from the Markov State Modelling (MSM), delineating structural hierarchy of chromatin organization with partitioning and effective interactions archetypal for corresponding levels of hierarchy. The stochastic embedding procedure (SEP) introduced in this work provides the 3D ensemble reconstruction, using effective interactions obtained by the MSM as the input. As a result, we obtain the structural ensemble of a genome, allowing one to model the functional and the cell-type variability in chromatin structure. The whole-genome reconstructions performed on the human B lymphoblastoid (GM12878) and lung fibroblast (IMR90) Hi-C data unravel distinctions in their morphologies and in spatial arrangement of intermingling chromosomal territories (CTs), paving the way to the studies of chromatin dynamics, developmental changes, and conformational transitions taking place in normal cells and during potential pathological developments