Using the UCSC Genome Browser, the HapMap site, and a number of software programs, (e.g. SNPStudio), we found that the region that includes rs2832407 has very low conservation across species and it is far from intron-exon boundaries. Despite evidence that it is not directly involved in splicing, LD patterns can be complex and many SNPs from recent genomewide association studies do not have apparent functional consequences. Consequently, this finding does not exclude the possibility that this SNP is functionally relevant to the AD phenotype and further investigation is needed to ascertain whether it has a direct effect on GluR5 kainate receptor function. An alternate explanation is that the association reflects linkage disequilibrium with functional variation elsewhere in the gene.
