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Russia may have yanked out U.S. government securities held at the Federal Reserve amid threats of economic sanctions if Russia enforces a Crimean referendum Sunday to break away from Ukraine.

The Fed said Friday that U.S. securities it holds in custody for other central banks fell to $3.21 billion -- the lowest level since December 2012 -- amid a record $106.1 billion drop in such holdings in the week that ended Wednesday. While traders say they suspect it was Russia, they don't know for sure, and it has not shown up on Russia's balance sheet.

Marc Chandler, chief Treasury strategist at Brown Brothers Harriman, said everything points to Russia, starting with the timing of the referendum and the potential for Western sanctions. He said rather than selling the Treasurys, Russia simply transferred them out of the U.S.

Pro-Russian volunteers gather in a square next to the Council of Ministers of Crimea's building, in Simferopol, two days ahead of the referendum over Crimea's bid to break away from Ukraine and join Russia.DANIEL LEAL OLIVAS / AFP - Getty Images

"Everything (Russian President Vladimir) Putin is doing is being extra cautious about retaliation, like bringing troops right to the Ukraine border," said Chandler. "The other reason I say it's most likely Russia is you look at the countries that have the largest reserves. It doesn't feel like it's China because China has enough on its plate."

Chandler said about half of Russia's foreign currency reserves are held in dollar-denominated instruments, and this would be about 80 percent of those dollar holdings.

"It could be somebody else, but it does seem circumstantial just on the timing alone," said Chandler.

He also said there are precedents for this type of behavior by Russia. He pointed to the birth of the Eurodollar market—dollars outside the U.S. In 1956, when the Soviet Union invaded Hungary, it feared the U.S. would retaliate with financial muscle, and Russia-based Narodny Bank shifted dollars from the U.S. and deposited them in its London branch, he noted.