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LncVar
 * 
 * lncRNA
   * Human
   * Mouse
   * Zebrafish
   * Fruitfly
   * Worm
   * Arabidopsis
   * Rat
   * Chicken
   * Cow
 * SNPs
   * Human
   * Mouse
   * Zebrafish
   * Fruitfly
   * Worm
   * Arabidopsis
 * CNVs
 * Fusions
   
 * Search
 * Download
 * Genome

 * Help
 * About


WELCOME TO LNCVAR !



SEARCH EXAMPLE | ADVANCED SEARCH



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.




SNPS & LNCRNA

 * 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

CNVS & LNCRNA

 * lncRNAs in CNV regions of various cancers
 * lncRNAs as prognostic biomarker candidates
 * Kaplan-Meier curves of lncRNAs

FUSIONS & LNCRNA

 * Predicted lncRNA gene involved fusion events




STATISTICS




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

Citation:
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)
Visitors:


For questions and suggestions, please contact: chenxiaowei@ibp.ac.cn   © LncVar.
Institute of Biophysics, Chinese Academy of Sciences.