All your income gets totaled on line 11.
Then the Standard Deduction or your Itemized Deductions are subtracted giving you the Taxable Income on line 15. The tax is on line 16.
The withholding shows up on line 25b and is subtracted from the Tax to give you a refund or more tax due.
You didn’t actually pay the tax or the 10% penalty (you pay a 10% early withdrawal penalty if you are under 59 ½). You had taxes withheld like from you paycheck. You still have to enter the whole gross amount (before taxes were withheld) with your other income to figure out the total tax (and it may put you into a higher tax bracket) and then the withholding is subtracted from the total tax to figure your refund or tax due. The Gross amount shows up on 1040 line 4a or 5a and the taxable amount on 4b/5b. The withholding will show up on 1040 line 25b.
