In addition to Article I, Section 9, see Article I, Section 2.
And Article IV, Section 2.
Of the original 13 slave states, 13 of them voted to incorporate slavery into the United States Constitution. This included New York, New Jersey, New Hampshire, Massachusetts, Delaware, Pennsylvania, Maryland, Rhode Island and Connecticut.
Also, Virginia, North and South Carolina, and Georgia. Don't ever forget to cast four-thirteenths responsibility in that direction.
I'm not saying all the northern states liked slavery. If the inclusion of slavery in the U.S. Constitution had not been in their political and economic best self interest, northern states may very well have voted to exclude it.
I would not consider any of those clauses as ratifying slavery, so much as living with it. For example, on the whole, the free states wanted slaves to be counted for taxation purposes, but not for determining allotment of representatives. The slave states wanted the reverse. Essentially, they split the difference. The result was not to anyone’s liking, but was a compromise the constitutional convention, and then the states, could put up with. The framers, like the Congress that issued the Declaration of Independence, recognized that they weren’t going to be able to sort out slavery, and that trying would just crash the entire effort to set up the Federal Government, so they came up with an accommodation everyone could put up with.