i have a SNP data that collected form two main phenotype defects how i can start analysing them please i want a step by step procedure if possible 

It's hard to provide help here "from square one," as it looks like you haven't done any work yourself to see what would be involved in this undertaking.

I'd recommend you google for "gwas tutorials", read them, and try different approaches on your own specific research question. Once you've tried a few things, you will have more specific/material questions that someone could have the hope of addressing. You can then bring those questions and provide background with what you have done and where you got stuck.

In the meantime, this post on Biostars was the first one that popped up for me when I searched for "gwas tutorial" and it looks like it will have some useful information for you that you can use to get started.