non-consistency when a locus does indeed have consistent biological effect across populations. For example, suppose a study in one population detects association at a single genotyped SNP but ignores correlates, so that only the same SNP is tested using logistic regression in a second population. This SNP may not appear to be consistent because of LD differences, whereas a correlated, causative SNP might have shown clear association in both populations, had it been genotyped and tested.
