We study complex Chern-Simons theory on a Seifert manifold $M_3$ by embedding it into string theory. We show that complex Chern-Simons theory on $M_3$ is equivalent to a topologically twisted supersymmetric theory and its partition function can be naturally regularized by turning on a mass parameter. We find that the dimensional reduction of this theory to 2d gives the low energy dynamics of vortices in four-dimensional gauge theory, the fact apparently overlooked in the vortex literature. We also generalize the relations between 1) the Verlinde algebra, 2) quantum cohomology of the Grassmannian, 3) Chern-Simons theory on $Sigmatimes S^1$ and 4) index of a spin$^c$ Dirac operator on the moduli space of flat connections to a new set of relations between 1) the equivariant Verlinde algebra for a complex group, 2) the equivariant quantum K-theory of the vortex moduli space, 3) complex Chern-Simons theory on $Sigma times S^1$ and 4) the equivariant index of a spin$^c$ Dirac operator on the moduli space of Higgs bundles.
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