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Table 4 List of all loci with significantly changed chromatin interactions after TNF stimulation and expression of associated genes after TNF stimulation

From: Functional genomics atlas of synovial fibroblasts defining rheumatoid arthritis heritability

Locus Interacting gene Base mean expression log2Fold Change lfcSE stat p value padj
12 SPRED2 772.22 − 0.34 0.08 − 4.36 1.29E−05 7.23E−05
19 SLC4A7 3702.62 − 0.23 0.13 − 1.80 0.072 0.145
20 PXK 1012.38 − 0.33 0.11 − 3.05 0.002 0.008
23 RBPJ 5319.00 0.56 0.22 2.51 0.012 0.032
24 IL6ST 18,850.31 0.72 0.08 8.91 4.91E19 2.30E17
30 TNFAIP3 7841.42 4.57 0.19 23.43 2.14E121 3.51E118
34 CDK6 4906.40 0.92 0.12 7.89 3.05E15 9.21E14
35 TNPO3 1671.71 0.05 0.07 0.76 0.449 0.597
41 PHF19 1065.75 0.71 0.14 5.09 3.56E07 2.74E06
42 TRAF1 1041.51 2.80 0.22 12.65 1.14E36 1.98E34
48 VPS37C 552.68 0.71 0.07 10.56 4.76E26 3.90E24
52 CDK2 648.74 0.85 0.13 6.69 2.23E11 3.72E10
52 RAB5B 1805.92 − 0.24 0.06 − 4.06 4.88E−05 2.42E−04
52 RNF41 1878.98 0.63 0.11 5.62 1.93E08 1.88E07
52 ANKRD52 1954.38 0.23 0.07 3.09 0.002 0.007
52 CNPY2 1033.14 0.37 0.07 5.30 1.16E−07 9.89E−07
52 PAN2 312.46 − 0.23 0.08 − 2.80 0.005 0.015
52 STAT2 4951.27 0.74 0.20 3.77 1.64E04 7.21E04
52 TIMELESS 728.81 1.11 0.14 8.10 5.66E16 1.87E14
52 GLS2 18.80 0.34 0.26 1.31 0.191 0.317
53 SLC26A10 10.97 − 0.29 0.39 − 0.75 0.455 0.603
53 OS9 5461.71 − 0.12 0.07 − 1.83 0.068 0.138
53 AGAP2 5.83 0.43 0.31 1.36 0.173 0.294
53 TSPAN31 370.51 − 0.29 0.11 − 2.56 0.010 0.028
53 CDK4 1630.73 0.06 0.07 0.88 0.378 0.529
53 AVIL 64.47 − 0.44 0.15 − 2.93 0.003 0.011
53 CTDSP2 3707.75 − 0.47 0.06 − 7.79 6.45E−15 1.85E−13
54 SH2B3 1493.15 0.52 0.10 5.29 1.25E07 1.06E06
54 ATXN2 781.23 − 0.05 0.08 − 0.71 0.478 0.625
64 ORMDL3 800.27 0.40 0.08 4.75 1.99E−06 1.32E−05
64 PSMD3 1842.20 0.18 0.05 3.66 2.53E−04 0.001
65;68 IFNAR2 644.38 2.81 0.11 26.14 1.14E150 2.92E147
68 IFNAR1 2355.18 0.95 0.08 12.55 3.95E36 6.53E34
68 IFNGR2 1248.98 1.10 0.08 12.90 4.71E38 9.03E36
68 ITSN1 1138.10 − 0.24 0.11 − 2.10 0.036 0.080
  1. Genes with a log2fold change > ± 0.5 and padj < 0.05 are marked in bold. lfcSE standard error for log2 fold change, stat statistic value for the null hypothesis, padj p value adjusted for multiple testing using Benjamini-Hochberg