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Vaughan was named interim manager alongside Darren Lyons at the end of January, following the departure of Jon Macken.
"It’s with a heavy heart that I’ve had to make the decision to bring my short spell with Radcliffe FC to an end.
"I’m unable at this time due to family commitments to devote the 100% required to represent such a fantastic football club.
"I would like to thank everybody at the club for their support and wish them every success in the future."
The club added: "Karl Marginson will be taking charge of the team in the interim."
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