Here we present the most comprehensive analysis yet of genetic and phenotypic data from human iPSC lines. Our study substantially extends on previous work6,7 by demonstrating widespread functional consequences of genetic variation for many molecular and cellular phenotypes in human pluripotent stem cell lines, including in the efficiency with which iPS cells differentiate41–43. This is potentially a consequence of variation in core components of the regulatory networks controlling cellular differentiation and responses to external environmental stimuli, as observed previously in hematopoietic cells and mouse and fly embryos44–46.
