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Margin interest is not included in the basis of your stock.
"If you borrow money to purchase an investment, you may qualify for a tax break. The IRS allows certain taxpayers to take a tax deduction for the interest expense on some loans using Form 4952. However, the tax ramifications of investment interest can be complicated, as the IRS only allows a deduction for certain types of investment interest. Additionally, the Alternative Minimum Tax (AMT) could completely disallow the use of your investment interest deduction."
You will have to claim the interest on FORM 4952.
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