The same analytic procedure was carried in polymorphic markers presented in the WTCCC hypertension dataset. Initially, we determined the set of markers from whom allelic frequencies were both directly genotyped and imputed using the haplotypic structure of flanking markers. The association statistics were generated and compared, similarly to the diabetes database approach, and similar results were also observed (Additional file 3, Table S2). Another important point is that, despite a considerably high correlation coefficient between association statistics, several hugely biased imputed markers could mislead follow up analyses. This finding appears rather contradictory but one should keep in mind that the correlation of minus log transformed association statistics is mainly defined by the immense number of markers showing good agreement between measures [9].
