Fig. 5

TNFAIP3 and IFNAR1 genetic risk loci—exemplary regions linked to TNF stimulation. Two exemplary risk regions where TNF stimulation had profound effects on chromatin structure and influenced the genetic regions containing RA SNPs. a The TNFAIP3 region on chromosome 6q23 (red arrow) containing RA credible SNPs (red lines, rs17264332 in Additional file 8: Table S5) changed from closed chromatin (light red bar) to open chromatin state (blue bar) after TNF stimulation and exhibited increased interactions with the promoter of TNFAIP3 in stimulated FLS (see also Table 4). b The genomic IFNGR2 region of the credible SNP set on chromosome 21 (rs73194058 in Additional file 8: Table S5, red arrow) interacted with several nearby genes. These interactions were further enhanced by TNF stimulation (see also Table 4). Chromatin at the IFNAR2 gene locus changed from a closed (light red bar) to open (blue bar) state in stimulated FLS. RNA-seq tracks show one randomly chosen RA hand, RA knee, and RA shoulder sample with (black) or without (gray) TNF stimulation