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"If I look at what happens to high-profile female footballers, to high-profile coloured footballers, and the abuse they take on social media... social media is a free-for-all," the former FA chairman said.
Clarke would later apologise for his remarks and the FA released a statement on Twitter after the hearing.
However, Clarke has now stepped down from his duties as FA chairman, saying that his "unacceptable words in front of Parliament were a disservice" to those involved with football.
He said in his statement: "As a person who loves football and has given decades of service to our game, it is right that I put the interests of football first.
"2020 has been a challenging year and I have been actively considering standing down for some time to make way for a new chair now our CEO transition is complete and excellent executive leadership under Mark Bullingham is established.
"My unacceptable words in front of Parliament were a disservice to our game and to those who watch, play, referee and administer it. This has crystallised my resolve to move on.
"I am deeply saddened that I have offended those diverse communities in football that I and others worked so hard to include.
"I would like to thank my friends and colleagues in the game for the wisdom and counsel they have shared over the years and resign from the FA with immediate effect."
The FA released a separate statement on its official website to say that Peter McCormick has been appointed interim chairman "with immediate effect."
The FA continued: "We would also like to reaffirm that as an organisation, we are absolutely committed to doing everything we can to promote diversity, address inequality and tackle all forms of discrimination in the game."
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