Functionnal fine-mapping

Hi,

I would like to perform functionnal fine mapping analysis on a Coronary Artery Disease (CAD) dataset (GWAS file available here : https://data.mendeley.com/datasets/gbbsrpx6bs/1), and specificaly using PAINTOR. 
Can I use your pipeline from this data ? The procedure to intergrate annotations is not clear.
Can you give me some clues about the command line to use?

Thanks for yor help