Analysis of LD Decay for Functionally Different Segments of the Human Genome

<div><p>(A) The graph shows average values of |D′| and their confidence limits (± standard deviation) as a function of the physical distance between SNPs for the following categories: (1) both SNPs reside in the same gene (blue line), (2) the SNPs reside in two different genes (green line), (3) both SNPs reside in the same intergenic region (red line), (4) one SNP resides in the gene and the other in the 30 kb upstream region of the same gene (purple line), and (5) one SNP resides in the gene and the other in the 30 kb downstream region of the same gene (gray line).</p><p>(B) Frequency distribution spectrum of |D′| values for SNP pairs at 100-kb distance. High |D′| values (>0.8) are overrepresented for equally spaced SNPs in a gene and its flanking regions as compared to intergenic regions.</p><p>(C) Frequency distribution of high LD values (|D′| > 0.5) for SNP pairs at 450-kb distance. Higher LD values are observed between a gene and its upstream region.</p><p>(D) Frequency distribution of high LD values (|D′| > 0.5) for SNP pairs at 650-kb distance. Higher LD values are observed between a gene and its upstream region.</p><p>The bin with |D′| = 1 is isolated to a separate bin in panels (B–D) as there is a considerable frequency bias for this |D′| value. Similar graphs plotted for separate human populations are available as <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020121#pgen-0020121-sg003" target="_blank">Figures S3</a>, <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020121#pgen-0020121-sg004" target="_blank">S4</a>, and S5.</p></div

Patterns of LD for Orthologous Genomic Segments of Approximately 5 Mb in Rat, Human, and Mouse

<p>LD plots for orthologous genomic segments in rat (A), human (B), and mouse (C) are shown. For each panel, the following information is shown: LD plot (top), haplotype blocks in SNP coordinates (middle), and physical map and haplotype blocks in physical coordinates (bottom). The haplotype map has a gradient representation for |D′| values that assists visual comparison of haplotype structure. Haplotype blocks were built with stringent criteria, sometimes resulting in splitting of visually recognized blocks. Three characteristic haplotype blocks that are conserved cross-species have been color-coded and are discussed in the text. Similar plots for a second mouse set, two other human populations, and the combined human set are available as <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020121#pgen-0020121-sg001" target="_blank">Figures S1</a> and <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020121#pgen-0020121-sg002" target="_blank">S2</a>.</p

Comparison of the Haplotype Block Densities between Syntenic Regions of Rat, Mouse, and Human (Same Genome Segments as Shown in Figure 1)

<p>The scatter plots show log₁₀ of the amount of haplotype blocks per 100-kb bin in rat (horizontal) against log₁₀ of the amount of haplotype blocks seen in syntenic region of mouse (A) and human (B) genome (vertical). Data points for gene-containing and intergenic genomic bins are shown as closed and open blocks, respectively. Observed correlations of haplotype block densities are significant in linear (<i>r</i> = +0.5530; <i>p</i> < 0.0001 [A] and <i>r</i> = +0.4563; <i>p</i> = 0.0005 [B]) as well as in log-transformed space (<i>r</i> = +0.6795; <i>p</i> < 0.0001 [A] and <i>r</i> = +0.3209; <i>p</i> = 0.0180 [B]).</p