Fig. 8: Linking RA chromatin classes to RA pathology.

a For each donor of the 14 donors shared between the unimodal scATAC-seq and AMP-RA reference studies with at least 200 T cells, the Pearson correlation coefficient (R) and two-sided p value (P) between the relative proportions of T cell chromatin classes defined in the unimodal scATAC-seq datasets (x axis) and classified into in the CITE-seq datasets through the multiome cells (y axis). b CNA correlations between myeloid cell neighborhoods and lymphoid density in AMP-RA reference myeloid cells visualized on chromatin class UMAP (top; two-sided global P = 0.005) and aggregated by classified myeloid chromatin classes (bottom). On the top, cells not passing the FDR threshold were colored grey. On the bottom, FDR thresholds shown in dotted black lines. c CNA correlations between T cell neighborhoods and CTAP-TB in AMP-RA reference T cells visualized on chromatin class UMAP (top; two-sided global P = 0.046) and aggregated by classified T cell chromatin classes (bottom). On the top, cells not passing the FDR threshold were colored grey. On the bottom, FDR thresholds shown in dotted black lines. d Scaled mean normalized chromatin accessibility for peaks that overlap putatively causal RA risk variants across chromatin classes in unimodal and multimodal datasets. Additional information is in Supplementary Table 5. e rs798000 locus, zoomed in (chr1: 116,735,799–116,740,800) (top) and zoomed out (chr1: 116,658,581–116,775,106) (bottom) with selected gene isoforms, SNPs, open chromatin peaks, and chromatin accessibility reads aggregated by chromatin class and scaled by read counts per class. STAT1/2 motif was downloaded from JASPAR¹⁰⁹ ID MA0517.1 and is not to scale, but it is aligned to the SNP-disrupting motif position.