LincSNP: a database of linking disease-associated SNPs to human large intergenic non-coding RNAs

作者：Shangwei Ning, Zuxianglan Zhao, Jingrun Ye, Peng Wang, Hui Zhi, Ronghong Li, Tingting Wang, Xia Li · 发表于：BMC Bioinformatics · 年份：2014 · DOI：10.1186/1471-2105-15-152 · 被引用次数：61 · 研究领域：Cancer-related molecular mechanisms research、Genetic Associations and Epidemiology、Genomics and Rare Diseases

BACKGROUND: Genome-wide association studies (GWAS) have successfully identified a large number of single nucleotide polymorphisms (SNPs) that are associated with a wide range of human diseases. However, many of these disease-associated SNPs are located in non-coding regions and have remained largely unexplained. Recent findings indicate that disease-associated SNPs in human large intergenic non-coding RNA (lincRNA) may lead to susceptibility to diseases through their effects on lincRNA expression. There is, therefore, a need to specifically record these SNPs and annotate them as potential candidates for disease. DESCRIPTION: We have built LincSNP, an integrated database, to identify and annotate disease-associated SNPs in human lincRNAs. The current release of LincSNP contains approximately 140,000 disease-associated SNPs (or linkage disequilibrium SNPs), which can be mapped to around 5,000 human lincRNAs, together with their comprehensive functional annotations. The database also contains annotated, experimentally supported SNP-lincRNA-disease associations and disease-associated lincRNAs. It provides flexible search options for data extraction and searches can be performed by disease/phenotype name, SNP ID, lincRNA name and chromosome region. In addition, we provide users with a link to download all the data from LincSNP and have developed a web interface for the submission of novel identified SNP-lincRNA-disease associations. CONCLUSIONS: The LincSNP database aims to integr...