Understanding how genetic variation affects cellular phenotypes is essential to better understand the causes of phenotypic variation and susceptibility to complex diseases. A well-studied cellular phenotype is gene expression and large numbers of expression quantitative trait loci (eQTL) studies have been performed nowadays. In my thesis, my first aim was to control the effect of a technical issue in RNA sequencing and eQTL studies, the effect of mapping bias to the reference genome to control for false positive associations Next, I aimed to better understand complex diseases by studying the transcriptome differences between healthy and disease and the genetic effects on gene expression in two different case-control studies. I studied Systemic Lupus Erythematosus (SLE), a chronic autoimmune disease of immense immunological and clinical heterogeneity. By using gene expression profiles, I aimed to understand the molecular heterogeneity and identify expression profiles that where different between SLE patients based on disease activity and severity. In the last project, I studied the response of gene expression after acute myocardial infarction. I aimed to understand the genetic regulation of gene expression, to map gene-environment interactions and finally to interpret the interplay between genetic variation, disease and GWAS findings.