Identification of a Systemic Lupus Erythematosus Susceptibility Locus at 11p13 between PDHX and CD44 in a Multiethnic Study Christopher J. Lessard, Indra.

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Identification of a Systemic Lupus Erythematosus Susceptibility Locus at 11p13 between PDHX and CD44 in a Multiethnic Study Christopher J. Lessard, Indra Adrianto, Jennifer A. Kelly, Kenneth M. Kaufman, Kiely M. Grundahl, Adam Adler, Adrienne H. Williams, Caroline J. Gallant, Juan-Manuel Anaya, Sang-Cheol Bae, Susan A. Boackle, Elizabeth E. Brown, Deh-Ming Chang, Lindsey A. Criswell, Jeffrey C. Edberg, Barry I. Freedman, Peter K. Gregersen, Gary S. Gilkeson, Chaim O. Jacob, Judith A. James, Diane L. Kamen, Robert P. Kimberly, Javier Martin, Joan T. Merrill, Timothy B. Niewold, So-Yeon Park, Michelle A. Petri, Bernardo A. Pons-Estel, Rosalind Ramsey-Goldman, John D. Reveille, Yeong Wook Song, Anne M. Stevens, Betty P. Tsao, Luis M. Vila, Timothy J. Vyse, Chack-Yung Yu, Joel M. Guthridge, Gail R. Bruner, Carl D. Langefeld, Courtney Montgomery, John B. Harley, R. Hal Scofield, Patrick M. Gaffney, Kathy L. Moser The American Journal of Human Genetics Volume 88, Issue 1, Pages 83-91 (January 2011) DOI: 10.1016/j.ajhg.2010.11.014 Copyright © 2011 The American Society of Human Genetics Terms and Conditions

Figure 1 Principal Components Identify Continental Ancestry Plot of the first two principal components identifying continental population substructure within our sample set before quality control (QC) (A) with 17,003 subjects and after QC (B) with 15,490 subjects. Each circle represents an individual sample, and colors represent the populations based on self-report. The American Journal of Human Genetics 2011 88, 83-91DOI: (10.1016/j.ajhg.2010.11.014) Copyright © 2011 The American Society of Human Genetics Terms and Conditions

Figure 2 Summary of Observed and Imputed SNPs Tested at 11p13 (A and B) Regional plot of observed (A) and imputed (B) SNPs displaying –log10(p) for an ∼300 kb window at 11p13 with approximate gene locations given at top. (A) Purple and red circles indicate results for SNPs observed in the replication study. The purple diamond and red square represent the meta-analysis results between the GWAS and the replication study. The symbol colors indicate the strength of LD with rs2732552, as given in the figure legend. Gray indicates that LD information was not available. The blue trace represents the average recombination rate for all races. (B) The purple diamond represents the most significant SNP after imputation, rs2553772, with strength of LD to rs2553772 indicated by symbol colors as given in the legend. (C) Expanded view of ∼14 kb haplotype associated with SLE in Europeans (blue diamonds), Asians (red squares), and African Americans (green triangles). Black lines indicate approximate location of transcription factor binding sites. Green and brown lines represent approximate location of methylated H3 histones. The American Journal of Human Genetics 2011 88, 83-91DOI: (10.1016/j.ajhg.2010.11.014) Copyright © 2011 The American Society of Human Genetics Terms and Conditions

Figure 3 Linkage Disequilibrium Patterns for the SNPs within the Associated Region Haplotype structure in Asians (A) and African Americans (B) from the data collected in this study. Diamonds show r2 values between markers, and those in solid black without a number are r2 = 1.0. Asian and European haplotype structure is nearly identical. The American Journal of Human Genetics 2011 88, 83-91DOI: (10.1016/j.ajhg.2010.11.014) Copyright © 2011 The American Society of Human Genetics Terms and Conditions