I'm having some trouble interpreting some GWAS and eQTL results and was hoping someone could help me out. In the genome there are haploblocks which are present in individuals and usually these haploblocks are separated by recombination hotspots (as far as I know). Using locuszoom (http://locuszoom.sph.umich.edu/locuszoom/ ) it is possible to create very nice plots that are commonly used to plot GWAS data for example http://www.nature.com/ng/journal/v45/n7/images/ng.2637-F1.jpg . I'm looking for a method to identify whether eQTL variants fall into the same haploblock of the gene or that the eQTL variant is more distant of the influenced gene and in another haploblock. So is there a cut off value of cM/Mb that I can use that is commonly accepted as a indicator for a new haploblock? or is there a way how I can change the cM/Mb number to another number that indicated the chance of a new haploblock?
Thanks in advance for any help..