what is linkage disequilibrium supposed to measure?
Linkage disequilibrium refers to a situation whereby two or more alleles, from different loci, segregate non-randomly. Therefore we have a statistical association between this two alleles.
The linkage disequilibrium can be used in gene mapping, because we assume that these loci are in the same region on the chromosome. The more often they appear together, the more they segregate non-randomly, the closer they should be on the chromosome.

http://www.researchgate.net/post/What_is_the_difference_between_Linkage_Equilibrium_and_Linkage_Disequilibrium