By combining linkage and association approaches, a disease loci position can be confined to a region finer than linkage analysis alone and avoid false positive association results due to admixture. Assuming the linkage is not over-estimated, if a measured variant is the actual functional variant affecting the phenotype and no other variants nearby confer any additional risk, linkage analysis conditional on the genotype of such a variant should provide no evidence for linkage. However if the suspected variant is in some degree of linkage disequilibrium with the actual causal variant, the evidence for linkage will be reduced proportional to the degree of LD.
