Gene Expression in Skin and Lymphoblastoid Cells: Refined Statistical Method Reveals Extensive Overlap in cis-eQTL Signals Jun Ding, Johann E. Gudjonsson,

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Gene Expression in Skin and Lymphoblastoid Cells: Refined Statistical Method Reveals Extensive Overlap in cis-eQTL Signals Jun Ding, Johann E. Gudjonsson, Liming Liang, Philip E. Stuart, Yun Li, Wei Chen, Michael Weichenthal, Eva Ellinghaus, Andre Franke, William Cookson, Rajan P. Nair, James T. Elder, Gonçalo R. Abecasis The American Journal of Human Genetics Volume 87, Issue 6, Pages 779-789 (December 2010) DOI: 10.1016/j.ajhg.2010.10.024 Copyright © 2010 The American Society of Human Genetics Terms and Conditions

Figure 1 Simplified Diagram for Categorization of Significant eQTLs from Study1 into Groups for the Estimation of the Overlap Percentage The American Journal of Human Genetics 2010 87, 779-789DOI: (10.1016/j.ajhg.2010.10.024) Copyright © 2010 The American Society of Human Genetics Terms and Conditions

Figure 2 Regional Plots for Evidence of cis-Association between SNPs and ERAP2 or RPS26 The most significant SNPs (the most significant SNP associated with ERAP2 in normal skin on the left panel; the most significant SNP associated with RPS26 in uninvolved skin on the right panel) are highlighted with a square. The other SNPs are drawn as circles and color coded according to the degree of linkage disequilibrium with the most significant SNP. The American Journal of Human Genetics 2010 87, 779-789DOI: (10.1016/j.ajhg.2010.10.024) Copyright © 2010 The American Society of Human Genetics Terms and Conditions

Figure 3 The Sharing of cis-eQTLs in Normal, Uninvolved, and Lesional Skin with the Other Two Types of Skin The p value threshold for discovery is 9 × 10−7, and the p value threshold for replication is 0.05. The American Journal of Human Genetics 2010 87, 779-789DOI: (10.1016/j.ajhg.2010.10.024) Copyright © 2010 The American Society of Human Genetics Terms and Conditions

Figure 4 Quantile-Quantile Plot of Psoriasis GWAS p Values for 389 Independent eQTL SNPs in Skin, with Confidence Intervals Defined by Non-eQTL SNPs The American Journal of Human Genetics 2010 87, 779-789DOI: (10.1016/j.ajhg.2010.10.024) Copyright © 2010 The American Society of Human Genetics Terms and Conditions