Mapping putative cis -variants acting on TLR9 gene expression. Allele transcript ratio mapping for 278 SNP across ~400 kb each side of the TLR9 gene. No association was found with any SNP surrounding the TLR9 gene. Y-axis represents the -log10 p-value and the x-axis the location in the chromosome. The horizontal dashed line indicates a nominal p-value of 0.01. The horizontal dashed and pointed line indicates the region-wide significance threshold of 1% calculated by performing 1000 permutations. The vertical dashed line indicates the position of the TLR9 transcribed SNP (rs352140). Each bullet represents a tested SNP. This data was obtained using the CEU data set. Similar results were obtained for the YRI.