Cell-to-cell heterogeneity in gene expression is a widespread phenomenon, and may play important roles in cellular differentiation, function and disease development. Human Cell Atlas aims to profile gene expression in every single human cells. Recent studies have implicated a potential role of chromatin in the heterogeneity in gene expression. Understanding the mechanisms of cellular heterogeneity requires simultaneous measurement of RNA and occupancy of histone modifications and transcription factors on chromatin due to their critical roles in transcriptional regulation.