Actually there are new approaches to study exactly that, and they are developing rapidly, cf: https://en.wikipedia.org/wiki/Chromosome_conformation_captur... Basically, this problem, along with a long list of other applications is being attacked by deep sequencing. The way it works is that you apply a treatment to DNA that 'glues' 3D contacts in place and covers the glued segment, apply restriction enzymes to cut out what's not covered by glue, get rid of the glue, sequence all that's left, and then map the remaining sequenced fragments to the reference genome. The output is the relative tendency of different regions to come into contact with each other.