LncSEA is a powerful platform that provides a variety of types of lncRNA sets for users and perform annotation and enrichment analysis of lncRNA sets based on lncRNA lists submited by users. We collected lncRNA sets from more than 20 associated lncRNA databases. We not only collected lncRNA sets based on downstream regulatory data sources but also calculated a large number of lncRNA sets regulated by upstream transcription factors (TFs) and DNA regulatory elements by integrating TF ChIP-seq, DNase-seq, ATAC-seq and H3K27ac ChIP-seq data associated with hundreds of human cell types. Importantly, LncSEA provides annotation and enrichment analysis functions of lncRNA sets. Moreover, lncRNA set enrichment analysis associated with upstream regulators and downstream targets of lncRNAs can be performed simultaneously when choosing the categories of both upstream and downstream reference sets. LncSEA also provides a user-friendly interface to search, browse and visualize detailed information about these lncRNA sets.