Long noncoding RNAs (lncRNAs) are emerging as key regulators for multiple essential biological processes involved in physiology and pathology. To explore the genome-wide lncRNA expression, we analyzed a compendium of 14,166 RNA-Seq libraries from 30 physiological tissues, 18 tumors and two cell lines from two independent data sets. In result, we identified 27,520 robust novel lncRNAs, largely expanding that catalog of human lncRNAs. Together with the known lncRNAs validated by our large-scale RNA-Seq samples, we presented the human lncRNA atlas (RefLnc) containing a total of 77,900 lncRNAs. Each lncRNA in the atlas is characterized by a panorama of sequence, expression and trait association. Through integrative analysis of the lncRNA expression profiles with phenotype and clinical outcome, we identified lncRNAs that are associated with physiological traits, cancer progression and clinical prognosis. All the genomic annotation and large-scale expression profiles are presented in an interactive open-access database, providing a resource for investigating the function of lncRNAs in human biology, cancer development, and for identifying lncRNAs with diagnostic and therapeutic potential.