Significance Gene expression is precisely controlled across human cell types to control cellular functions and phenotypes. Here we present a technology to quantify the level of expression of genes in single cells, which will help to understand how genes are regulated in each cell type in the human body. We demonstrate that this technology improves upon existing tools to enable understanding how DNA regulatory elements control gene expression and mapping the frequencies of different cell types in tissues. This technology will enable new large-scale studies to understand gene control.