Association results and SNP annotations in the <i>1q23 CD84</i> locus.

<p>A) Regional association plots with ΔDAS (top panel) and with <i>CD84</i> expression (bottom panel), showing strengths of association (−Log10 P-value) versus position (Kb) along chromosome 1. B) Schematic of <i>CD84</i> gene structure (RefSeq gene model, box exons connected by diagonal lines, arrow indicates direction of transcription) with strong enhancer chromatin states (orange rectangles) and SNPs in high LD (r2>0.8) with rs6427528 (vertical ticks). SNPs in enhancers are labeled below. C) Annotations of strong-enhancer rs6427528 proxy SNPs; listed are SNP rs-ID (major and minor alleles), conservation score, cell line with DNAse footprint if present, and transcription factor binding sites altered. 1- Genomic evolutionary rate profiling (GERP) conservation score, where a score >2 indicates conservation across mammals. 2- DNase footprint data are compiled from publicly available experiments by HaploReg. 3- Position weight matrix logos show transcription factor consensus binding sites with nucleotide bases proportional to binding importance. SNP position is boxed. Note that the rs10797077 AIRE_2 and the rs6427528 SREBP_4 motifs are on the minus strand (base complements correspond to SNP alleles), with the SREBP motif shown upside down to align with the rs6427528 KROX motif on the positive strand. Data are from HaploReg.</p

<i>CD84</i> expression level and clinical features.

<p>Analyses are shown in RA patients from the BRASS and ABCoN registries, for baseline DAS (top panel, n = 210; R² = 0.02, p = 0.02) and ΔDAS (bottom panel, n = 31; R² = 0.001, p = 0.46). Best-fit linear regression lines are shown in black, with shaded regions showing linear regression model (slope and intercept) 95% confidence intervals. <i>CD84</i> expression levels were quantile normalized, and ΔDAS values were adjusted for age, gender and baseline DAS.</p

GWAS results for the ΔDAS phenotype.

<p>Shown are strengths of association (−Log10 P-value) for each SNP versus position along chromosomes 1 to 22. A) All samples (n = 2,706). B) Etanercept-treated patients (n = 733). C) Infliximab-treated patients (n = 894). D) Adalimumab-treated patients (n = 1,071).</p