Is the $10k limit for Roth IRA withdrawals to buy a home a limit for earnings or also for contributions? If I close a $12k Roth IRA to buy a home is $2k penalized?

I've had the Roth IRA for more than 5 years and it's not through my employer. The mutual fund won't let me take out just $10,000 - they said I can take out 10% or 90% of the total $12k