In summary, our study provides a detailed picture of the genetic and phenotypic variability in human pluripotent stem cells, including the major drivers of this variation. Data and cell lines from this study are being made available through www.hipsci.org, the European Collection of Authenticated Cell Cultures (ECACC) and the European Bank for Induced Pluripotent Stem Cells (EBiSC). As the HipSci resource continues to expand in sample size and assays, it will enable the study of subtler genetic effects, under a wider range of conditions, in an increasing range of disease-relevant differentiated cell types.