In case you are worried your game's progress data is not transferred to Steam's cloud system correctly and would like to create a backup of your save files - here is where they are located by default: 

.\Steam\userdata\USERID(e.g. 472815306)\488730 (this is a fixed SteamID of the game)

Note that since God's Trigger uses the Steam Cloud Savegame system, your save files will be automatically downloaded to any computer when you log into your Steam Account.

Your save files are stored under a unique folder name based on you SteamID, which means they will not be overwritten by any other Steam User profile.