Novel single nucleotide polymorphisms in the human small inducible cytokine A3 (SCYA3) gene are described. In addition, various genotypes, haplotypes and haplotype pairs for the SCYA3 gene that exist in the population are described. Compositions and methods for haplotyping and/or genotyping the SCYA3 gene in an individual are also disclosed. Polynucleotides containing one or more of the SCYA3 polymorphisms disclosed herein are also described.