Xamarin, KendoUI, PhoneGap, Cordova are all frameworks that utilize HTML5, CSS, and JavaScript to create apps that are portable to Android, Web, Windows Phone, BlackBerry and iOS. You need to find a framework like that. In order to compile for iOS/iPhone you need a Mac, but to develop you'll need one of those frameworks above. There is no native way of modifying in Windows, and compiling. Of course you could edit .m and .h files in a standard text editor, but you can't debug or compile unless you are in XCode on a Mac.
Unity3D/Unreal Engine 4 you can work in Windows, and it'll output the iOS XCode Project files, and source code. But you'll still need a Mac to compile it. One of the strict requirements by our friends at Apple.
Once the app is compiled you can submit to the App Store via Application Loader or directly in XCode. I've also heard people submit to the app store via Windows once it is compiled, but haven't done this myself.
