Nondeductible SEP-IRA contributions are not permitted. If you reported nondeductible contributions, they were reported as regular individual traditional IRA contributions, not SEP-IRA contributions. Regardless, all of your traditional IRAs, including SEP and SIMPLE IRAs must be combined when calculating the proportion of a distribution from your traditional IRAs that is a nontaxable distribution of basis in nondeductible contributions. Only if your basis exceeds the total of your 2016 year balances in IRA plus distributions from your IRAs in 2016 would the distributions be entirely nontaxable.
There *is* a method that can be used to separate the basis from the before-tax money in your IRAs that involves rolling over the before-tax money to your 401(k), but the complexities are beyond the scope of this forum.
