Fruitfly-SNPs :

• SNPs in transcription factor binding sites (TFBS) in promoters of lncRNA genes. TFBS were identified from ChIP-seq data and were also predicted by using TF position weight matrix from JASPAR database. SNPs in TFBS might affect the transcription of lncRNAs.
• SNPs in TFBS that were co-located with promoters of lncRNA genes in spatial organization. We combined TFBS with genome spatial contacts, and found that TFBS were co-located with the promoter of lncRNA genes in spatial organization. SNPs in these TFBS might affect transcription of lncRNAs through long-range looping interactions.
• Synonymous and nonsynonymous SNPs in lncRNAs, which were found to be able to encode peptides. We collected the information of peptides encoded by lncRNAs from literatures, and identified the SNPs that might alter peptide sequences.