Hull manager Phil Brown had accused Spaniard Fabregas of spitting at the feet of Horton in the tunnel of the Emirates Stadium after Arsenal's 2-1 FA Cup quarter-final victory on Tuesday.
"We are aware of the allegations but are waiting for the report from referee Mike Riley, or if there is any complaint from Hull City," an FA spokesman said on Wednesday.
Fabregas strongly denied spitting at anyone.
"I categorically deny that I spat at anybody after the match," Fabregas, who did not play because of injury, said in a statement on Arsenal's website.
"I have never done this in my whole career on the pitch, so why would I do it when I am not even playing?
"I can understand the frustration of losing a game to a dubious goal, that has happened to me many times in my career as well. But this is not the fault of me or any of the Arsenal players."
Brown said he had watched Fabregas spitting near his assistant manager.
"I was there and I witnessed it, he spat at my assistant manager down the tunnel," Brown had said at a post-match news conference after William Gallas's controversial late header knocked his side out of the Cup.
Brown added: "He spat at his feet."
Arsenal manager Wenger said he had not witnessed any incidents at the end of the game.
"I went early and haven't seen anything," he told reporters. "I don't know what he has seen. I'm sorry I cannot speak of something I have not seen."
The managers did not shake hands at the end of a stormy match. Wenger accused Hull of wasting time "from the first minute". Brown was furious that Gallas's goal, which appeared to be offside, had been allowed to stand.
