How do I enter 1099-S proceeds from real estate transactions with expenses?

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Your 1099-S sales are reported as the sale of an investment Schedule D. Where asked for the Cost or other basis enter your purchase price plus the cost of any improvements / expenses of the sale.

To enter an investment sale other than from a brokerage account (1099-B), follow the steps below.

In your Federal return, choose the tab for Wages & Income
Scroll down to Investment Income and Show more
Start/Revisit Stocks, Mutual Funds, Bonds, Other
On the next screen, say Yes or select Add More Sales
On the next screen, choose No
On the next screen, choose the correct option and Continue with the section until it completes.