Fig. 4

GWAS enrichment and macrophage chromatin state. a Enrichment of GWAS risk SNPs that are located in differential ATACs amongst each trait relative to other traits (1,379 EFO term). The horizontal green dash line represents the Bonferroni-adjusted p value of 0.05. b Bar plots showing the enrichment of the annotations of macrophage differential ATACs (green), non-differential ATACs (black) and the top5 (enrichment p values) baseline LD score models (grey) in GWAS signals for Crohn’s disease, ulcerative colitis, inflammatory bowel disease traits, multiple sclerosis or BMI. Bars are ordered by enrichment magnitude in each trait. Error bars represent jackknife standard errors around the estimates of enrichment as described in [24]. #: FDR < 0.05 after correction for all the annotations tested. n.s: not significant. c Chord Diagram of GWAS SNPs (either leads or proxies) in differential ATAC regions that associate with differential risk to immune disorders. ATACs were assigned to expressed genes through their genomic locations (nearest RefSeq genes). The connecting lines indicate the lead SNPs for each GWAS association of different studies. The cyan and grey dots indicate the median odds ratios and median –log10 p values of the associations, respectively. Colours in circle above cyan dots represent the linked immune traits. The differentially expressed genes in HD vs. UT and/or LDHD vs. HD are highlighted in blue. AD, autoimmune disease; AE, atopic eczema; ALG, allergy; AR, allergic rhinitis; AS, ankylosing spondylitis; ATD, autoimmune thyroid disease; BE, Barrett’s esophagus; CD, celiac disease; CHC, chronic hepatitis C virus infection; CL, cholelithiasis; CRO, Crohn’s disease; CVI, common variable immunodeficiency; DC, dental caries; GAS, Gallstones; GD, Graves’ disease; HB, hepatitis B virus infection; IBD, inflammatory bowel disease; JIA, juvenile idiopathic arthritis; KD, mucocutaneous lymph node syndrome; MS, multiple sclerosis; PSA, psoriatic arthritis; PSO, psoriasis; RA, rheumatoid arthritis; SC, sclerosing cholangitis; SJIA, systemic juvenile idiopathic arthritis; SJO, Sjogren’s syndrome; SLE, systemic lupus erythematosus; slgAD, selective IgA deficiency disease; UC, ulcerative colitis; VIT, vitiligo. See also Fig. S3