I don't think a native speaker would use #3. You will hear #1 and 2, but in my opinion they are incorrect. CB
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nkspb1) I will tell you what are the reasonsI will tell you what the reasons are.
nkspb2) He knows which is the best option.2) He knows what the best option is.
nkspb3) I don't know what is it.3) I don't know what it is.
nkspb1) I will tell you what are the reasons2) He knows which is the best option.3) I don't know what is it.These wordings are commonly use by people who are learning English and therefore, make them stand out as non-native speakers.