Off topic:Tools To Define Cis-Regulatory Modules And Associate Them To A Nearby Gene?

Question

[Ahdf-Lell-Kocks]

I would like to know of tools to define cis-regulatory modules for one or multiple TF ChIP-seq experiments that would take into account the inter-peak distance and the distance to the nearest gene at the same time when defining CRMs from the ChIP-seq dataset. What I've seen up until now are tools that first assign each peak to the nearest transcription start site and then define CRMs by setting a threshold for inter-peak distance within the peaks previously associated to a given TSS.

I would be interested in a tool that combines both distances, inter-peak distance and distance to upstream and downstream TSSs, at the same time.