I will describe two projects that aim to better dissect the causal chain from functional genetic variant through molecular intermediates and finally to organismal trait or disease risk. In the first, we are using pooled profiling of RNA binding protein (RBPs, splice factors) binding across individuals to measure and then computationally model genetic effects on both binding and RNA splicing. In the second, we have developed a causal network inference method that scales to hundreds of nodes by leveraging convex optimization.