Prion

One of my friends heard back today from a Ph.D. program she interviewed at a while ago, letting her know she was accepted. There's hope. If you can, shoot the program coordinators for the programs you are waiting for an email. 

First, I will echo what others have said: you will get out of your PhD what you put into it. The program you choose needs to be right for you. Look for PIs doing work you want to do. Forget courses, forget everything other than the work being done and whether or not it's the type of work that will keep you up at night. 
If both programs fit your needs, think about SF vs NYC. Rent is ridiculous in SF, but it's also high in NYC. However, I believe Columbia provides subsidized housing in Washington Heights. Does SF provide affordable housing? In general, it seems like there are west coast people and east coast people. If you know which type you are, the choice should be easy. 
As far as science goes, I was under the impression that Columbia pretty much invented modern genetics. Depending on the type of genetics you like, Columbia could be a great fit. In my mind, as someone reading papers everyday, I see more biochemistry coming out of UCSF. I'll just say, there are some amazing publications coming out of UCSF. There are also outstanding PIs coming out of UCSF. 
In the end, you're in a really great position and you will be happy either way. Ask yourself, 1) If my top three choices for labs don't work out, will I be happy with my fourth choice?, 2) Do I see myself living in NYC or SF for five or so years? 
I know this post is unorganized and prattling. I've had way too much coffee today. But I hope the general ideas are conveyed. Feel free to PM me if you would like bounce around ideas. 
Congratulations, regardless! You're in a very fortunate position. 

Coming from someone who is currently waitlisted at Columbia, I'll try to be unbiased.
Looking at your previous posts, it looks like you may be overthinking your decision. They both have great programs, but you will only get out what you put in to the program. My best advice would be to go with your gut feeling. It is difficult to rank a program based on others view of the program.

Two quick points to follow up on some of the conversations here.
 
1. If you are wait-listed, other people declining will rarely move you into the "admitted" zone. Every accepted individual has until April 15th to decline, which is when you also need to accept your acceptances to be safe. Because schools accept more people than they plan to have matriculate to get their desired class sizes, you need to consider that you might only be called off the wait-list only in some catastrophic circumstance, and most likely after April 15th. So if you're betting on this, think very carefully about your other options. Additionally, cajoling people into speeding up their thought processes in figuring out which school to attend is uncalled for; though, on the flip side, I did let go of schools after all my interviews were done if I couldn't see myself "going there," so people don't need to hoard schools that they know they ultimately won't go to.
 
2. Interviews are not only a test of fit for yourself, but also for the program honestly (as they'll be making close to half a million dollar investment in your education, at the minimum). Interviewers are coordinated by the best of the ability by a program's admin, so sometimes getting someone that you didn't want or ask for, or getting grilled, wasn't actually the intention by the admin - it just ended up that way. As stated above, the admins know which professors are known to grill. This is usually frowned down upon in the grand scheme of things. Students with overwhelmingly bad interviews get rejected, but out of each interview panel, there tends to be one professor with veto abilities (this can go for or against you). What people tend to forget is that the hosting students also have a say; while the right review from a PI is enough to get you in, an overwhelmingly negative response from a bunch of students will also likely get you rejected.  

I'll be declining for sure, so fingers crossed I can get you off the waitlist

I've been waitlisted for Columbia's integrated CMBS program and it is my top choice!! If you are not planning on attending I am begging for you to let them know as soon as possible! I am praying to still get accepted if people decline their offer! 

Columbia CMBS admissions offer!