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Having taxes withheld does not change that taxable amount of the gross distribution shown in box 1 of the Form 1099-R, since federal taxes must be paid with money that has already been taxed. The tax withholding is simply a pre-payment toward the tax liability eventually shown on your tax return. You get credit for this prepayment on Form 1040 line 64 or Form 1040A line 40.
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