Genome wide association studies are widely used to identify disease loci. However, due to extensive local linkage disequilibrium it is still an open challenge to elucidate the molecular mechanisms that underlie such loci. Since most of the known sequence variation is located in intergenic regions, it is a plausible hypothesis that these variants affect cis regulatory elements. Expression quantitative trait locus (eQTL) experiments can shed light on which genes are likely targets affected by regulatory polymorphisms. We showed how to use this information in order to identify the core components of gene regulatory networks, namely transcription factor (TF) – target relations by predicting which TF is affected in its binding affinity by variants in cis regulatory elements. Secondly, we investigated the role of TFs as effectors of trans regulatory variants using eQTL data. Moreover we showed how these regulatory networks can be used to interpret human disease associations. Histone posttranslational modifications tag regulatory elements in the genome and can be used in order to restrict the search space for regulatory elements. Thus in a third project, we analyzed the relation between sequence variants, chromatin states and gene expression.