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Well the San Francisco Bay Area has a train system called BART (Bay Area Rapid Transit) that can get you into the city in about an hour or less from most parts of the Bay Area. The glaring exception is San Jose, although there have been talks of a BART extension going to San Jose for YEARS.
BART is a great system, but it's gotten a bit dirty and you don't want to ride BART through certain stops after a certain hour. If that's something you can put up with, however, then there are many great places to live. One obvious question is, what is your price point?
If you do decide to live in San Francisco, there is quite a range of places to live and price points. If you decide to live in the Sunset District, you'll be further away from most of the high paying jobs and the "City," but you'll probably find a place a little more affordable. If you're into the nightlife and want to actually live IN the city, then SOMA (South of Market) and North Beach areas would be awesome, but expect to pay quite a bit of money.
I personally grew up in Fremont which is a beautiful city about a 45 minute drive from San Francisco. It has a BART Station that will take you straight into the city, and is also about 20-30 minutes from San Jose. Let me know if you have any questions.
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