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You enter the SEP contributions in the Business tab of TurboTax under "Less Common Business Situations" at the line called "Self-employed retirement". Note that this description is from TurboTax Home & Business (desktop); TurboTax Self-Employed may be laid out a little differently.
If you are self-employed and have an SEP-IRA, then the retirement plan at your employer does not affect your SEP-IRA contribution.
If you are an employee and you have both a 401(k) and SEP IRA through your employer, your deferral contribution to the 401(k) cannot exceed $18,000 ($24,000 if over 50), and the total contributions to both accounts cannot exceed $53,000 ($59,000 including 401(k) catch-up contributions).
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