The long non-coding RNAs (lncRNAs) make up most of the ncRNAs. LncRNAs are non-coding transcripts more than 200 nucleotides long; they have an exon-intron-exon structure, similar to protein-coding genes, but do not encompass open-reading frames. There is mounting evidence that lncRNAs participate in a wide-range of biological processes, such as regulation of epigenetic signatures and gene expression, maintenance of pluripotency, and differentiation of embryonic stem cells. In addition, several individual lncRNAs have also been implicated in human diseases. Many genome-wide association studies (GWAS) have mapped disease-associated genetic variants (SNPs) to, or in the vicinity of, such lncRNA regions. However, it is not clear how these SNPs affect the disease. We tested whether SNPs were also associated with the lncRNA expression levels in five different primary human tissues and observed that there is a strong correlation between genotype and lncRNA expression.