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Long noncoding RNAs (lncRNAs) have been identified in various species, and play essential roles in many molecular processes. Genetic variations, including single nucleotide polymorphisms (SNPs) and structural variations, are widely distributed in the genome. Variations in the long noncoding gene loci may affect lncRNA transcripts from sequences, structures, expression levels to biological functions.Therefore we constructed LncVar, a database of long noncoding genes associated genetic variations in 6 species (human, mouse, zebrafish, worm, fruitfly, Arabidopsis). It contains:

      LncRNAs are from NONCODEv4. Conservation of lncRNAs among the 6 species are calculated by two methods (PhastCons and liftOver).
      SNPs in transcription factors binding sites (TFBS) of lncRNA promoters (TFBS were obtained from either ChIP-seq data or prediction).
      SNPs in TFBS that are spatially co-located with lncRNA promoters in DNA 3D organization (DNA 3D organization was based on 5C,Hi-C and DNase Hi-C data).
      SNPs in m6A modification regions of lncRNAs (m6A modification were from m6A-seq).
      SNPs in open reading frames of lncRNAs that could encode peptides (data from ribosome profiling).
      eQTLs of lncRNA genes (data from literatures).
      LncRNAs in Copy Number Variation Regions as prognostic biomarker candidates of various cancers (CNV, RNA-seq and clinical data are from TCGA).
      LncRNA genes involved fusion events predicted from RNA-seq data of 7 cell lines from the ENCODE project.

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  • SNPs in TFBS of lncRNA gene promoters
  • SNPs in TFBS spatially co-located with lncRNA promoters
  • SNPs in m6A modification region of lncRNAs
  • SNPs in ORF of lncRNAs
  • eQTLs of lncRNA genes
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  • lncRNAs in CNV regions of various cancers
  • lncRNAs as prognostic biomarker candidates
  • Kaplan-Meier curves of lncRNAs
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Fusions & LncRNA

  • Predicted lncRNA gene involved fusion events


  Tips: Click the legends to show or hide the species!

1. Chen X., et al. LncVar: a database of genetic variation associated with long non-coding genes. Bioinformatics. 2017 Jan 1;33(1):112-118.
2. Chen X., et al. LncVar: Deciphering Genetic Variations Associated with Long Noncoding Genes. Methods Mol Biol. 2019;1870:189-198.
LncVar database is supported by National Natural Science Foundation of China (31701122, 31871307 and 31801072)