In this thesis, the regulation of gene expression is analyzed in three different aspects. At first by understanding how the genetic variation has a downstream effect on gene expression through the variation of activity of regulatory elements, such as promoters and enhancers. In particular, we identified cases of promoters compensation with no evidence of differences in the total gene expression. In the second part of the thesis we investigated the cellular variability of gene expression in two different contexts: firstly, we studied the X chromosome inactivation (XCI) happening in female individuals. We observe extensive heterogeneity of this mechanism within and between individuals and tissues. And secondly, we integrated single-cell gene expression quantification and DNA variation to identify cell-type specific expression quantitative trait loci (eQTLs) in the human pancreatic islets.