You're not giving us much detail to go on, but fundamentally with a single case and a single control you will have very little to work with no matter what kind of assay you have performed.
If by single you mean you have one case sample and one control sample, then the answer is no. Under a standard analysis, you would like to test the hypothesis that a given locus is associated with disease more frequently than you would expect to see by chance. Even if you assume your genotypes are perfect, that there is a SNP associated with your disease, and that this SNP is in a coding region, you will see many polymorphisms by chance between any two humans. You have no basis for asserting that any particular SNP is definitely associated with disease, even if that SNP is found only in your case, not in dbSNP, etc. You will expect to see even gene-truncating mutations even in normal humans (see the recent 1000 genomes papers for some quantification of this), so identifying a mutation that ablates a given gene's function only in your case would not be definitive (though it may suggest a candidate). This is the reason why genome-wide association studies require thousands of cases and controls for common, non-familial diseases.
As a special case, there are Mendelian diseases where possession of a single mutation in a coding region is causal for the disease with complete penetrance. Even in that case, you will still at best be generating a very large list of candidate mutations. In those cases the most powerful approach is usually to use family pedigrees to identify loci linked to disease (thus the name linkage studies). You will expect to see mutations introducing stop codons even in normal humans (see the recent 1000 genomes papers for some quantification of this), so identifying a mutation that ablates a given gene's function only in your case would not be informative with only one case.
Assuming the most straightforward reading of your third question, to get some answers on linking genotype and phenotype, the answer is yes, it can be done. Start with an introductory genetics textbook.