I think you just have to remember them, I don't know whether there is any rules. なんで なんでも なんじ なんねん なにが なにを なにも

In general, you read 何 as "nani" when it is placed before a particle and "nan" when combined with です or a counter like じ or さい for example. 1 - これは何ですか。(kore wa nan desu ka) - What is this? 2- 何はこれ。(nani WA kore)- What is this? The meaning is the same, but the reading is different. In other cases.. お前は何をしているの。(omae wa nani WO shiteiru no) - What are you doing? [informal] 君の弟はなんさいですか。- (kimi no otouto wa nansai desu ka) -How old is your younger brother? In your sentence.. ここに何がありますか。- (koko ni nani GA arimasuka) Ga is a particle and 何 is coming before it, so you read as NANI.