Retirement tax questions

But I have already been paying income taxes on the rest of my income throughout the year... That is what is so confusing. Wouldn't I just pay the income tax on the outstanding loan amount which $45,000 and according to the 2018 IRS tax brackets, that is 12% when filing married/jointly. I do believe the penalty is 10% which would be $4,500. Sorry. This is all super confusing!