You can't file an extension after you file your original return. It should have been rejected.
At this point, prepare an amended return. Add the new information. An amended return is a complete copy of your entire tax return, with the corrected information, plus form 1040X which is a cover page that summarizes the changes. Print, sign and mail the amended return to the address indicated on the instruction page. You will likely also have to file an amended state return if the 1099-R changed your taxable income. Include a check for your payment or make an online payment at www.irs.gov/payments.
You should expect to get a bill from the IRS for late fees and interest. Don't accept Turbotax's suggestion to calculate the penalty for you since it is almost always off by a few dollars and you end up getting a bill anyway. If this is the first time you have owed a penalty, you can request an abatement when you get the bill (but the interest can't be abated.)
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