I have two SNPs - one on Chr-11 and another on Chr-15 - for which I have to see the epistatic effect on a phenotype. I know it makes no sense to see the epistasis for two SNPs that are close enough to have significant LD but in my case even though they are far away from each other, their LD measures are highly significant (D' - 0.99; p
If the SNPs are actually on different chromosomes then they will be unlinked, as chromosomes are segregated independently during meiosis.
If you *do* have a high LD score (do you have r^2 as well?), then it suggests something odd is going on (e.g. bad annotation, gene duplication, bad SNP assay, chromosomal rearrangements).
Sure! You can measure Linkage Disequilibrium between two SNPs on two different chromosomes. While two SNPs on different chromosomes can not be physically linked, they can still be in Linkage Disequilibrium. Physical linkage (two genes that are close and located on the same chromosome) is a specific case of Linkage Disequilibrium. For example, two genes that are on different chromosomes are not physically but they might be in Linkage Disequilibrium with one another, if they are both under selection or they are both required to show a given phenotype. Also, the maximum r value in physical linkage is 0.5, where in LD it can go up to 1.
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