The Texans officially announced the move minutes later.
The Texans made Clowney, who played college football at South Carolina, the No. 1 overall selection in 2014. He has accumulated nine-or-more sacks over the past two seasons.
Clowney has compiled 205 combined tackles, 29 sacks, 11 passes defensed, and five forced fumbles over his five NFL seasons.
The San Francisco 49ers hope to address their pass rush this offseason. The team ranked No. 22 in sacks this past season.
"I think that's a need for us," general manager John Lynch told Colin Cowherd last week. "It's a need for a lot of people. When you say a need, you usually think you're really bad. I just look at it as that's just one piece that's missing from an area where we can become a tough team to deal with.
"We've got guys like DeForest Buckner, and Arik Armstead, and Solomon Thomas inside. If you put that edge presence, I think we can become a unit that is tough to deal with."
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