Input: The inputs are predicted variants (SNPs, insertions, deletions
and MNPs). The input file is usually obtained as a result of a
sequencing experiment, and it is usually in variant call format (VCF).
Output: SnpEff analyzes the input variants. It annotates the variants
and calculates the effects they produce on known genes (e.g. amino
acid changes). A list of effects and annotations that SnpEff can
calculate can be found here.
As a rule, no, there is not totally in silico way to predict that. You would have to see if someone has empirically tried to correlate SNPs in that approximate position with expression. This might be feasible in a species like mice, where the genetics are a bit simpler, since the mice come from inbred strains.
I suppose you could try and see if your SNPs sits on a known regulation site, and how much your SNPs changes that site from the canonical consensus sequence.
But if you are looking for a simple function where you put your SNP in, and biological consequences like expression changes come out, no, that doesn't exist.