Table II.
CIT identifies genes for which DNAm likely mediates RA genetic risk
| Gene | CpG | Lead meQTL SNP | Bayes colocalization PP4∗ | Locus | CIT P value | CIT Permutation FDR |
|---|---|---|---|---|---|---|
| CD4+T cell | ||||||
| ANKRD55 | cg21124310 | rs6859219 | 1.00 | 5q11.2 | 1.11 × 10−4 | 7.06 × 10−4 |
| cg10404427 | rs6859219 | 1.00 | .0057 | 0.0044 | ||
| cg23343972 | rs6859219 | 1.00 | .0062 | 0.0069 | ||
| cg15431103 | rs6859219 | 0.95 | .0496 | 0.0319 | ||
| JAZF1 | cg07522171 | rs2189966 | 0.97 | 7p15.1 | 3.97 × 10−4 | 0.0035 |
| cg11187739 | rs4722758 | 0.99 | .0035 | 0.0044 | ||
| cg16130019 | rs917117 | 0.99 | .0529 | 0.0319 | ||
| ORMDL3 | cg18711369 | rs12946510 | 0.86 | 17q12 | 4.46 × 10−4 | 0.0035 |
| cg10909506 | rs12946510 | 0.93 | .0016 | 0.0044 | ||
| FCRL3 | cg17134153 | rs2210913 | 0.99 | 1q23.1 | .0027 | 0.0044 |
| cg01045635 | rs2210913 | 0.99 | .0120 | 0.0296 | ||
| IL6ST | cg15431103 | rs6859219 | 0.95 | 5q11.2 | .0100 | 0.0296 |
| cg15667493 | rs6859219 | 0.99 | .0139 | 0.0296 | ||
| cg10404427 | rs6859219 | 1.00 | .0216 | 0.0305 | ||
| cg21124310 | rs6859219 | 1.00 | .0349 | 0.0305 | ||
| cg23343972 | rs6859219 | 1.00 | .0352 | 0.0305 | ||
| C11orf10 | cg16213375 | rs61897793 | 1.00 | 11q12.2 | .0163 | 0.0296 |
| TAX1BP1 | cg11187739 | rs4722758 | 0.99 | 7p15.1 | .0470 | 0.0305 |
| GSDMB | cg18711369 | rs12946510 | 0.86 | 17q12 | .0277 | 0.0305 |
| cg10909506 | rs12946510 | 0.93 | .0448 | 0.0305 | ||
| B cell | ||||||
| FCRL3 | cg19602479 | rs2210913 | 0.99 | 1q23.1 | 4.69 × 10−4 | 0.0420 |
| cg01045635 | rs7522061 | 0.97 | 5.49 × 10−4 | 0.0420 | ||
| CCR6 | cg15222091 | rs3093025 | 0.98 | 6q27 | .0101 | 0.0966 |
| cg19954286 | rs3093025 | 0.98 | .0258 | 0.1330 | ||
| cg05094429 | rs3093025 | 0.96 | .0347 | 0.1330 | ||
| IKZF3 | cg18691862 | rs9903250 | 0.44 | 17q12 | .0249 | 0.1330 |
| ORMDL3 | cg12749226 | rs11557466 | 0.97 | 17q12 | .0249 | 0.1330 |
For the top results in CD4+ T cells and B cells, we report the raw omnibus CIT P value, and FDR value calculated using 1000 permutations.44 Here, we report all instances of P < .05, highlighting those that satisfy the FDR 0.05 threshold. In instances whereby CIT implicates multiple Illumina probes for the same gene, we report the most statistically significant probe. Results from all CITs across both cell types are available in Tables E17 and E18.
PP4 from the Bayesian colocalization analysis38 reports the previous probability that the associations with RA susceptibility and DNAm levels shared the same common genetic variant; only reported where PP4/PP3 > 5 (see this article’s Methods section in the Online Repository at www.jacionline.org).