  We consider the $S^3\times S^1$ superconformal index $\mathcal{I}(\tau)$ of
4d $\mathcal{N}=1$ gauge theories. The Hamiltonian index is defined in a
standard manner as the Witten index with a chemical potential $\tau$ coupled to
a combination of angular momenta on $S^3$ and the $U(1)$ R-charge. We develop
the all-order asymptotic expansion of the index as $q = e^{2 \pi i \tau}$
approaches a root of unity, i.e. as $\widetilde \tau \equiv m \tau + n \to 0$,
with $m,n$ relatively prime integers. The asymptotic expansion of
$\log\mathcal{I}(\tau)$ has terms of the form $\widetilde \tau^k$, $k = -2, -1,
0, 1$. We determine the coefficients of the $k=-2,-1,1$ terms from the gauge
theory data, and provide evidence that the $k=0$ term is determined by the
Chern-Simons partition function on $S^3/\mathbb{Z}_m$. We explain these
findings from the point of view of the 3d theory obtained by reducing the 4d
gauge theory on the $S^1$. The supersymmetric functional integral of the 3d
theory takes the form of a matrix integral over the dynamical 3d fields, with
an effective action given by supersymmetrized Chern-Simons couplings of
background and dynamical gauge fields. The singular terms in the $\widetilde
\tau \to 0$ expansion (dictating the growth of the 4d index) are governed by
the background Chern-Simons couplings. The constant term has a background piece
as well as a piece given by the localized functional integral over the
dynamical 3d gauge multiplet. The linear term arises from the supersymmetric
Casimir energy factor needed to go between the functional integral and the
Hamiltonian index.
