  Chromospherically sensitive atomic lines display different spectra in stellar
active regions, spots, and the photosphere, raising the possibility that
exoplanet transmission spectra are contaminated by the contrast between various
portions of the stellar disk. To explore this effect, we performed transit
simulations of G and K-type stars for the spectral lines Ca II K at 3933 \AA,
Na I 5890 \AA, H I 6563 \AA\ (H$\alpha$), and He I 10830 \AA. We find that
strong facular emission and large coverage fractions can contribute a
non-negligible amount to transmission spectra, especially for H$\alpha$, Ca II
K, and Na I D, while spots and filaments are comparatively unimportant. The
amount of contamination depends strongly on the location of the active regions
and the intrinsic emission strength. In particular, active regions must be
concentrated along the transit chord in order to produce a consistent
in-transit signal. Mean absorption signatures in Na I and H$\alpha$ for
example, can reach $\approx 0.2\%$ and $0.3\%$, respectively, for transits of
active latitudes with line emission similar in strength to moderate solar
flares. Transmission spectra of planets transiting active stars, such as HD
189733, are likely contaminated by the contrast effect, although the tight
constraints on active region geometry and emission strength make it unlikely
that consistent in-transit signatures are due entirely to the contrast effect.
He I 10830 \AA\ is not strongly affected and absorption signatures are likely
diluted, rather than enhanced, by stellar activity. He I 10830 \AA\ should thus
be considered a priority for probing extended atmospheres, even in the case of
active stars.
