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Rejection of the tax, which was a condition of a European bailout, eased worries that savers will begin withdrawing funds. At the same time, it left efforts to rescue the country - the latest casualty of the euro-zone debt crisis - up in the air.
"Regardless of the vote in Cyprus, we still have the problem. No one knows: 'What is the Cypriot financial restructuring going to look like?' sad Nicholas Colas, chief market strategist at the ConvergEx Group, in New York.
Banks in Cyprus will remain closed until Thursday.
The S&P 500's retreat followed a long streak of gains where the index came close to hitting its all-time closing high set in 2007. The S&P 500 is still on track to post its best quarter in a year. The benchmark S&P 500 is up 8.4% for the year, while the Dow is up 10.3%.
Energy shares led the day's decline following a drop in oil prices and a slide in the shares of oil services companies. The PHLX oil services sector index dropped 2%. Shares of Schlumberger Ltd
The Dow Jones industrial average edged up 3.76 points, or 0.03%, to 14,455.82 at the close.
The Standard & Poor's 500 Index fell 3.76 points, or 0.24%, to finish at 1,548.34. The Nasdaq Composite Index slipped 8.50 points, or 0.26%, to close at 3,229.10.
In volatile trading, the Dow made a swing of 132.25 points from its session high to its intraday low.
During the session, the S&P 500 traded as low as 1,538.57.
Strategists expect the S&P 500 to still break above its record high reached in October 2007, but they expect the rally to slow from there. A Reuters poll of equity strategists surveyed over the past week put the S&P 500 at 1,600 by year end, above its October 9, 2007, all-time closing high of 1,565.15. The Dow initially surpassed its 2007 record levels on March 5 and then set nominal record closing highs on subsequent session through the close on March 14.
On Monday, Goldman Sachs increased its year-end target for the S&P 500 to 1,625 while Morgan Stanley raised its target to 1,600.
The day's declining shares included Electronic Arts Inc
Shares of Cliffs Natural Resources Inc
Among the day's gainers, Walgreen Co
Walgreen shares hit $45.80, their highest since September 2007, and closed at $44.74, up 5.4%. Amerisource gained 3.6% to $50.06. In contrast, Cardinal lost 8.2% to $42.35.
European bank shares extended Monday's decline, with the sector's index down 2.1% on Tuesday.
"Whether the deposit levy occurs or not, the fact that it was agreed to by the EU means that claims on private property are not out of bounds, which pretty much says that nothing is out of bounds," said Fred Copper, senior portfolio manager, international equity, at Boston-based Columbia Management, in reference to the banking crisis in Cyprus.
US economic data added to upbeat views on the housing sector. Housing starts data showed that groundbreaking to build new US homes climbed in February and new permits for construction rose to their highest since 2008, in a sign the US housing market's recovery was building momentum.
The PHLX housing sector index rose 0.3% to end at 191.79, after earlier climbing to 194.41 - its highest level since late July 2007.
Volume was roughly 6.8 billion shares traded on the New York Stock Exchange, the Nasdaq and the NYSE MKT, compared with the 2012 average daily closing volume of about 6.45 billion.
Decliners outpaced advancers on the NYSE by about 17 to 13, while on the Nasdaq, seven stocks fell for every five that rose.
