The Structure of Haplotype Blocks in the Human Genome Stacey B. Gabriel, Stephen F. Schaffner, Huy Nguyen, Jamie M. Moore, Jessica Roy, Brendan Blumenstiel, John Higgins, Matthew DeFelice, Amy Lochner, Maura Faggart, Shau Neen Liu-Cordero, Charles Rotimi, Adebowale Adeyemo, Richard Cooper, Ryk Ward, Eric S. Lander, Mark J. Daly, David Altshuler

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Supplemental Figure 1. Allele frequency scatter for pairs of populations. The corresponding FST value is indicated on each plot. (A) Yuroban as compared to European; (B) Asian as compared to European; (C) Yuroban as compared to Asian and (D) Yuroban as compared to African-American. (E) The correlation in the diference in allele frequency for the two non-African population samples as compared to the Yoruban sample. The difference in allele frequendcy between the European and Yoruban sample is highly correlated to the difference between the Asian and Yoruban sample, indicating a common history for the two non-African samples.

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Supplemental Figure 2. Block-like structure of linkage disequilibrium across four populations. Pairwise D' values for pairs of markers within each population sample: (A) Yoruban, (B) African American, (C) European, (D) Asian. Block diagrams include SNPs with frequency >20% in the given population. Black squares indicate strong LD (as defined in text); white squares, strong evidence for recombination; gray squares, all other uninformative comparisons.

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Supplemental Figure 3. Haplotype frequencies within blocks as estimated by the EM algorithm. Haplotype frequencies based on phased data versus unphased data from the same individuals.

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