Volume 155, Issue 1, Pages (July 2018)

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Volume 155, Issue 1, Pages 168-179 (July 2018) Female-Specific Association Between Variants on Chromosome 9 and Self-Reported Diagnosis of Irritable Bowel Syndrome Ferdinando Bonfiglio, Tenghao Zheng, Koldo Garcia-Etxebarria, Fatemeh Hadizadeh, Luis Bujanda, Francesca Bresso, Lars Agreus, Anna Andreasson, Aldona Dlugosz, Greger Lindberg, Peter T. Schmidt, Pontus Karling, Bodil Ohlsson, Magnus Simren, Susanna Walter, Gerardo Nardone, Rosario Cuomo, Paolo Usai-Satta, Francesca Galeazzi, Matteo Neri, Piero Portincasa, Massimo Bellini, Giovanni Barbara, Anna Latiano, Matthias Hübenthal, Vincent Thijs, Mihai G. Netea, Daisy Jonkers, Lin Chang, Emeran A. Mayer, Mira M. Wouters, Guy Boeckxstaens, Michael Camilleri, Andre Franke, Alexandra Zhernakova, Mauro D’Amato Gastroenterology Volume 155, Issue 1, Pages 168-179 (July 2018) DOI: 10.1053/j.gastro.2018.03.064 Copyright © 2018 AGA Institute Terms and Conditions

Gastroenterology 2018 155, 168-179DOI: (10.1053/j.gastro.2018.03.064) Copyright © 2018 AGA Institute Terms and Conditions

Figure 1 Manhattan plot of GWAS results and regional plots for the 9q31.2 locus. Top panel: GWAS association signals (-log10 P) are reported for SNP markers across all chromosomes, shown in alternate colors. Significance levels corresponding to genome wide (P = 5.0 × 10–8) and suggestive (P = 5.0 × 10–6) thresholds are indicated, respectively, with red and blue horizontal dashed lines. For each independent association signal, the nearest gene (mapping closest to the tag SNP) is reported, together with the number of additional genes from the same locus (in brackets). Bottom panel: 9q31.2 locus-specific regional plots of association signals in the entire UK Biobank cohort, and in sex-stratified analyses. SNPs are color-coded to reflect their linkage disequilibrium (r2) with the tag SNP rs10512344 (diamond symbol) according to the color key in the upper left corner. Gastroenterology 2018 155, 168-179DOI: (10.1053/j.gastro.2018.03.064) Copyright © 2018 AGA Institute Terms and Conditions

Figure 2 FUMA analysis of GWAS results. (A) GWAS risk loci (P < 5.0 × 10–6) with tag SNPs and FUMA annotations. The genome-wide significant locus 9q31.2 is highlighted in bold. (B) Gene set enrichment analysis significant findings (ranked based on false discovery rate–adjusted P value) and color-coded categories GO molecular function (GO_mf), miRNA targets (microRNA_targets), and transcription factor targets from the Molecular Signature Database (TF_targets). Gastroenterology 2018 155, 168-179DOI: (10.1053/j.gastro.2018.03.064) Copyright © 2018 AGA Institute Terms and Conditions

Figure 3 Haplotype association and conditional analysis. (A) Summary statistics from association tests between IBS/AAM tag SNPs haplotypes and IBS in UK Biobank (females only). FREQ, haplotype frequency; OR, odds ratio; P, P value. (B) Regional plot of the 9q31.2 locus before and after conditional analysis on AAM. The horizontal dashed line shows the genome-wide significance P value threshold (5.0 × 10–8). Gray and blue circles correspond to unconditioned and AAM-conditioned P values, respectively. Gastroenterology 2018 155, 168-179DOI: (10.1053/j.gastro.2018.03.064) Copyright © 2018 AGA Institute Terms and Conditions