What kind of trip are you looking for? Food, brewpubs, cocktail bars, touristy things, hikes, etc?
Regarding where to stay, Union Square is safe. Tenderloin is pretty sketch at night but during the day and early evenings, there are a lot of great restaurants and bars there. Outside of Tenderloin, the only other places that are a bit sketch is area near 6th and Mission St, and pockets of Mission districts.
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