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The London Stock Exchange last week effectively scuppered a planned merger with Deutsche Boerse to create Europe's biggest exchange, by rejecting an EU demand to sell a trading platform in Italy.
Faber, who chairs Deutsche Boerse's supervisory board, told a German newspaper the Brexit vote had created strong headwinds for the 29 billion euro ($30.8 billion) deal.
"We didn't know for months what the British wanted. And in the end, the dual headquarters that we wanted was an absolute no-go," he told Frankfurter Allgemeine Sonntagszeitung.
Sources had previously told Reuters that the question over the location of the headquarters worried LSE executives.
Faber also told the paper that Deutsche Boerse CEO Carsten Kengeter had his backing.
"He is and remains the right person to head the company, the right CEO, in order to drive the growth of Deutsche Boerse," Faber said. "That's why we got him on board and we will work on it together."
Reporting by Victoria Bryan; Editing by Clelia Oziel