This work was supported by an MRC Clinician Scientist Fellowship (MR/N008340/1) to P.R., a Wellcome Trust Senior Research Fellowship in Clinical Science (ref. 103749) to N.C.H., an AbbVie Future Therapeutics and Technologies Division grant to N.C.H., a Guts UK–Children’s Liver Disease Foundation grant (ref. R43927) to N.C.H., a Tenovus Scotland grant (ref. E18/05) to R.D. and N.C.H. and British Heart Foundation grants (RM/17/3/33381; RE/18/5/34216) to N.C.H. R.V.-T. was funded by EMBO and Human Frontiers long-term fellowships. C.J.W. was funded by a BBSRC New Investigator Award (BB/N018869/1). P.N.N., C.J.W. and N.T.L. are funded by the NIHR Birmingham Biomedical Research Centre at the University Hospitals Birmingham NHS Foundation Trust and the University of Birmingham. This paper presents independent research supported by the NIHR Birmingham Biomedical Research Centre at the University Hospitals Birmingham NHS Foundation Trust and the University of Birmingham. The views expressed are those of the author(s) and not necessarily those of the NHS, the NIHR or the Department of Health and Social Care. J.P.I. is funded by the NIHR Bristol Biomedical Research Centre, University Hospitals Bristol Foundation Trust and the University of Bristol. C.P.P. was funded by the UK Medical Research Council, MC_UU_00007/15. This work was also supported by Wellcome Sanger core funding (WT206194). We thank the patients who donated liver tissue and blood for this study. We thank J. Davidson, C. Ibbotson, J. Black and A. Baird of the Scottish Liver Transplant Unit and the research nurses of the Wellcome Trust Clinical Research Facility for assistance with consenting patients for this study. We thank the liver transplant coordinators and surgeons of the Scottish Liver Transplant Unit and the surgeons and staff of the Hepatobiliary Surgical Unit, Royal Infirmary of Edinburgh for assistance in procuring human liver samples. We thank S. Johnston, W. Ramsay and M. Pattison for technical assistance with FACS and flow cytometry. We thank J. Henderson for technical support and G. Muirhead for assistance with isolation of liver endothelial cells. This publication is part of the Human Cell Atlas (www.humancellatlas.org/publications).