1)He was absent. Do you know what is the reason why?
2)He was late. Do you know what the reason is?/ Do you know what is the reason?
.......................
I'm not a teacher
.......................
What is the reason? - direct question
Do you know
what the reason is? - embedded question (a question included in another sentence)
When you're dealing with an embedded question you need to change the word order to that of a statement (not a question).
Other examples of embedded questions:
-
Could you tell me where I can find the bus station? (NOT *... where can I find the bus station?)
-
I was wondering if you would like to go with me? (NOT *... if would you like to go with me)
-
I would like to know where she is. (NOT *... where is she.)
-
I don't know what she said. (NOT *... what did she say.)