I would be thankful for any valuable suggestion, 

in fact I use Cas9 to KO my lncRNA with average length 7kb, around 220nt were deleted and after selection of single cell clone, validation of KO by PCR and Sanger sequence, I extract RNA, and test with qRT-PCR 3 different primeres were used one targeting the KO site and the other 2 one upstream and the second downstream  only the primer which target the 200bp that were deleted nearly has no expression compared to control while other primers no difference, is this logic?? and then after KD of this lncRNA using 5 shRNAs each targeting 200 bp, with 5 specific qRT-PCR primers, the KD was significantly, and some of TFs were significantly correlated changes with thier downstream genes,  while after KO of these 220 bp non of these TFs or thier downstream genes where changed??

please, any help how to answer the following questions,  does the qRT result is logic after KO, and why non of these TFs changes after deletion of these 220bp any other suggestion i would appreciate 

thanks