Income tax is paid on all net taxable income, whereas self-employment taxes are only paid on 1099 income.
Self-employment taxes represent your expected contributions to Social Security and Medicare. These are typically paid by an employer as part of their payroll tax burden.
Deductions to your 1099 income reduce both your income tax and self-employment tax burden but remember that your income taxes are calculated on your total income, including any non-1099 sources.