In this self-contained book, following Edward Witten, Maxim Kontsevich, Greg Kuperberg, and Dylan Thurston, we define an invariant Z of framed links in rational homology 3-spheres, and we study its properties. The invariant Z, which is often called the perturbative expansion of the Chern-Simons theory, is valued in a graded space generated by Jacobi diagrams. It counts embeddings of this kind of unitrivalent graphs in the ambient manifold, in a sense explained in the book, using integrals over configuration spaces, or, in a dual way, algebraic intersections in the same configuration spaces. When the ambient manifold is the standard 3-sphere, the invariant Z is a universal Vassiliev link invariant studied by many authors including Guadagnini, Martellini and Mintchev, Bar-Natan, Bott and Taubes, Altsch\"uler and Freidel, Thurston, and Poirier... This book contains a more flexible definition of this invariant. We extend Z to a functor on a category of framed tangles in rational homology cylinders and we describe the behaviour of this functor under various operations including some cabling operations. We also compute iterated derivatives of our extended invariant with respect to the discrete derivatives associated to the main theories of finite type invariants. Together with recent results of Massuyeau and Moussard, our computations imply that the restriction of Z to rational homology 3-spheres (equipped with empty links) contains the same information as the Le-Murakami-Ohtsuki LMO invariant for these manifolds. They also imply that the degree one part of Z is the Casson-Walker invariant.