I am performing a GWAS Analysis, while comparing my pre-imputation and post-imputation data, I observed that the most significant genetic variant (p<1x 10-16) from pre-imputation data is no more significant post imputation. Imputation performed using reference genome 1000genome phase3 v5 SAS population data in Michigan Imputation server. These variants were missed out while matching the target data and the ref data. How do I overcome this? What is should be reported in the manuscript (pre or post imputation data)? How do we justify such findings ?