To identify potential functional variants that might contribute to associations with the phenotype, we reassembled >300 kb sequences at the PPP3CA locus. We searched these sequences for simple sequence repeats and SNPs, relying on alignments of genomic BAC and EST sequences from NCBI and Celera. We identified several simple sequence length poly-morphism/microsatellite markers. A trinucleotide repeat lies in PPP3CA's 5′untranslated region (UTR) (ss68756203). We observed six and seven GCC allellic variants, containing between 2 and 10 repeat, in European and African–American samples, respectively. A 16 nucleotide tandem repeat (ss68756205) with eight nucleotide insertion lies in intron 1. A pentanucleotide repeat (ss68756204) lies in intron 3. The SNP now termed rs2850328 lies in 5′ flanking putative promoter sequences [Figure 1(A)]. Several of these markers were used in genotyping assays (see above and below) to identify allele frequency differences between disease and control samples.
