To identify factors influencing the location of untaggable SNPs we considered their distribution relative to segmental duplications, repeat sequence, CpG dinucleotide density, regions of low SNP density, unusual allele frequency distribution, linkage disequilibrium patterns and recombination hotspots. We find no evidence for an enrichment of untaggable SNPs in segmental duplications or repeat sequence, as would be expected from mis-mapping of SNPs (2% and 35% of common SNPs lie in segmental duplications and repeat sequence, respectively, compared to 1.8% and 29%, respectively, of untaggable SNPs). Untaggable SNPs are slightly enriched in CpG islands (0.37% of common SNPs are in CpG islands compared to 1.4% of untaggable SNPs) and have slightly reduced MAF (Fig. 4). Most notably, untaggable SNPs are strongly enriched in regions of low linkage disequilibrium, particularly in recombination hotspots. To test whether these untaggable SNPs are themselves responsible for the identification of recombination hotspots, we eliminated them from 100 randomly chosen recombination hotspots and reassessed the evidence for a local peak in recombination. In all cases we still find evidence for a considerable increase in local recombination rate.
