Our genetic code is stored in our DNA, which consists of four bases: adenine (A), cytosine (C) guanine (G) and thymine (T). More than three billion of these bases are strung together in 23 chromosomes, forming our genome. Each of our cells has two copies of our genome, containing instructions that guide cellular processes such as growth, development, signalling, and many more, but can occasionally also be the basis of disease. A large part of the genetic instructions are contained in our genes, which are small regions in our genome which contain information to make ribonucleic acid molecules (RNA), which can be translated to proteins. Variation in our genomes can change the regulation of genes or the functionality of the protein products. The work in this thesis shows the effects of genetic variation on the activity (the amount of RNA that is produced) of genes. Often, the effect of genetic variation differs between tissues and cell types. We developed a method to study the difference in genetic regulation between different cell types and applied this to samples taken from brain and blood. We show that there are large differences in genetic regulation between brain and blood, and we identify putatively causal disease genes for several neuro-psychiatric disease which could not be identified using only data from blood. This thesis expanded our knowledge of the difference in genetic regulation of gene expression between brain and blood, which can help us in further understanding genetic diseases and in designing drug targets.