GCTA-COJO with very dense imputation panel (HRC)

My initial GWAS meta-analysis resulted in 4 genome-wide significant loci on 4 different chromosomes. Running GCTA-COJO only revealed multiple independent signals on these 4 chromosomes at genome-wide significance, which is encouraging. However, there are between 178 and 303 "independent" signals resulting from the COJO analysis on each of these chromosomes, which seems like a lot. I am wondering if this can be due to the use of the Haplotype Reference Consortium (HRC) panel? Looking at the results, the vast majority of the signals have a frequency of <0.05. 

Thank you for your insight!