You can deduct the interest in your rental activity expenses. As long as the loan proceeds from your HELOC secured by your primary residence, are used to buy, build or improve the rental property itself then it is deductible as other interest. If it had been secured by the rental home then it would be mortgage interest.
When you are entering your expenses for the rental property, you can select to add 'Other Interest' and include the amount from your HELOC. See the image below for both TurboTax Online and TurboTax CD/Download.