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If you view the worksheet supporting Line 4 Business use of your home of IRS Form 2106 Employee Business Expenses, you will see that the direct portion of Mortgage Interest and Real Estate Taxes flows to Line 4 of Form 2106, but the indirect portion does not. The indirect portion is on Lines 6 and 10 of the federal Schedule A where it is not subject to the 2% limit it would be subject to on Line 21 of the Schedule A.

This is consistent with the instructions in IRS Publication 587 Business Use of Your Home, page 20: 

Deductible mortgage interest. If you file Schedule C (Form 1040), enter all your deductible mortgage interest on line 10 of Form 8829. After you have figured the business part of the mortgage interest on lines 12 and 13, subtract that amount from the total on line 10. The remainder is deductible on Schedule A (Form 1040), line 10 or 11. If the interest you deduct on Schedule A for your home mortgage is limited, enter the excess on line 16 of Form 8829.

If you file Schedule F (Form 1040), include the business part of your deductible home mortgage interest with your total business use of the home expenses on line 32 of Schedule F (Form 1040). Enter "Business Use of Home" on the dotted line beside the entry. You can use the Worksheet To Figure the Deduction for Business Use of Your Home, later in Pub. 587, to figure the deductible part of mortgage interest. Enter the non-business part of the deductible mortgage interest on Schedule A, line 10 or 11. To determine if the limits on qualified home mortgage interest apply to you, see the instructions for Schedule A (Form 1040) or Publication 936.

Real estate taxes. If you file Schedule C (Form 1040), enter all your deductible real estate taxes on Form 8829, line 11. After you have figured the business part of your taxes on lines 12 and 13, subtract that amount from your total real estate taxes on line 11. The remainder is deductible on Schedule A (Form 1040), line 6. If you file Schedule F (Form 1040), include the business part of real estate taxes with your total business use of the home expenses on line 32. Enter the non-business part of your real estate taxes on line 6 of Schedule A.

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