At the NEGR1 locus, we found that the 10-kb deletion, the 45-kb deletion and the reference structural allele at NEGR1 each have perfect tagging SNPs (r2 = 1.0) in the HapMap CEU sample. In constructing Figure 4c, we colored each SNP according to which of these structural-allele-tagging SNPs it showed the strongest LD with in HapMap CEU. Locations of conserved elements were obtained from the phastConsElements17way track of the UCSC Genome Browser. A threshold score of 300 was set for inclusion in this figure.
