This is the dataset for the publication of A Reference Tissue Atlas for the Human Kidney from the Kidney Precision Medicine Project (KPMP). KPMP is building a spatially-specified human kidney tissue atlas in health and disease with single-cell resolution. Here, we describe the construction of an integrated reference map of cells, pathways and genes using unaffected regions of nephrectomy tissues and undiseased human biopsies from 56 subjects. We use single-cell/nucleus transcriptomics, subsegmental laser-microdissection transcriptomics and proteomics, near-single-cell proteomics, 3-D and CODEX imaging, and spatial metabolomics to hierarchically identify genes, pathways and cells. Integrated data from these different technologies coherently identify cell types/subtypes within different nephron segments and the interstitium. These profiles describe cell-level functional organization of the kidney following its physiological functions and link cell subtypes to genes, proteins, metabolites and pathways. They further show that mRNA levels along the nephron are congruent with the subsegmental physiological activity. This reference atlas provides a framework for classification of kidney disease when multiple molecular mechanisms underlie convergent clinical phenotypes.