In this thesis, we were interested in better understanding the relationship between the coding and non coding part of the genome, specifically between non-coding regulatory variants, transposable elements (TEs) and genes. In the first part, we investigated the causal relationship between expression Quantitative Trait loci (eQTL) variants, TEs and genes in colorectal cancer samples and discovered 1,758 TEs impacting the expression of 1,626 genes, specifically in cancer. In the second part of this thesis, we were interested in better characterising the role of transposable elements in the regulation of gene expression in adult somatic tissues. For this, we used the Genotype-Tissue Expression (GTEx) project to understand how TEs mediate genetic effects, altering the expression of nearby genes in 43 different adult tissues. We discovered 28,888 TEs affecting the expression of 12,599 nearby genes and showed that the effects of these TEs on nearby genes is shared among closely related tissues.