I didn't find any related info in the faq. So I want to know whether it will affect either my reputation or the OP's reputation when I ‘flag’ a comment, question or answer. Will it result in decreasing his reputation?
I know this isn't my home meta, but I want to chime in here as a mod on the site the OP is most active on.
As Evpok says, flags don't directly affect reputation (the number). But they can affect a user's personal reputation (what the site and its mods think of a user). Moderators review every one of your flags, taking appropriate action and noting whether the flags were helpful or not. (A flag can be helpful even if mods don't take action based on it.) You can see the number of flags that have been marked helpful in your own profile, and clicking the number takes you to a flag summary page (here's yours on Seasoned Advice), showing the flags you've submitted and how they were all handled. So if someone's flags are all helpful, moderators will naturally notice it and appreciate it. And on the other extreme, if a user submits tons of unhelpful flags, it eats up the mods' time and they won't be happy.
So in terms of practical advice: flag whatever you think should be flagged, and mods will handle it appropriately. As long as you're not doing something insane (flagging all of one user's posts), nothing bad will come of it, and if you're doing the site a service, we're all happier for it.
It doesn't per se. Flagging affects a specific flag score that you can see in your profile under helpul flags. The flags are used to request moderator attention, mostly for technical issues, not for Q&A quality.
However, if your flag trigger a moderator action, it can indirectly affect reputation, e.g. if it results in question closing.