You do not report the income and expenses from a rental property in your self-directed IRA on your personal tax return.
Reporting income and expenses in a self-directed IRA have to follow strict rules and any errors may lead to fines and tax consequences. Please ask your IRA trustee.
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If you receive a letter from the IRS about the 1099 for the rental property that is part of a Self-Directed IRA the trustee for your IRA can help you resolve it with the IRS.