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

Shangwei Ning, Zuxianglan Zhao, Jingrun Ye, Peng Wang, Hui Zhi, Ronghong Li, Tingting Wang and Xia Li*

Author Affiliations

College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China

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BMC Bioinformatics 2014, 15:152  doi:10.1186/1471-2105-15-152

Published: 20 May 2014



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.


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.


The LincSNP database aims to integrate disease-associated SNPs and human lincRNAs, which will be an important resource for the investigation of the functions and mechanisms of lincRNAs in human disease. The database is available at webcite.

LincRNA; Disease-associated SNPs; GWAS; Non-coding RNA; Database