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The answer you are looking for is in the name of the building.
World Trade Center.
The Pentagon is the seat of military power for the United States, and the White House is the seat of Political power for the United States, but the World Trade Center, when it stood, was a bustling and busy tower that stood as a testament and as a focal point for the Economic Power of the United States.
It certainly had an effect in that regard. (Pardon the Wikipedia reference, but it is quite complete on the economic impact of the attack).