Long noncoding RNAs (lncRNAs) are RNAs that do not code for any protein, and could act functionally as a transcript. Recent evidence suggests that lncRNA genes could be more prevalent than protein coding genes. However, the function of these molecules is only understood for a very small fraction of them. Here we present an overview of lncRNAs, and attempt to systematically identify structural features within lncRNAs, and look for disruptive SNPs (single-nucleotide polymorphisms) that could alter their stability. In particular, we have identified numerous disease-associated SNPs that alter structures of lncRNAs, and give insight to their function.