The significant genes for RA risk in both cross-tissue and single-tissue TWAS analysis
| Gene | CytoBand | BP0 | BP1 | UTMOST_Discovery | FUSION_Replication | Reported | ||||
| PUTMOST | PFDR | Top GWAS ID | Z score | PFUSION | PFDR | |||||
| PTPN22 | 1p13.2 | 114 356 433 | 114 414 381 | 1.82E-11 | 1.19E-08 | rs2476601 | 6.75 | 1.51E-11 | 2.03E-09 | Yes |
| INPP5B | 1p34.3 | 38 326 369 | 38 412 729 | 1.24E-09 | 5.06E-07 | rs28411352 | 4.98 | 6.29E-07 | 5.77E-05 | Yes |
| ATP13A2 | 1p36.13 | 17 312 453 | 17 338 423 | 2.84E-04 | 2.13E-02 | rs2240335 | 3.81 | 1.39E-04 | 8.44E-03 | Yes |
| MMEL1 | 1p36.32 | 2 522 078 | 2 564 481 | 1.04E-08 | 3.57E-06 | rs2843401 | 4.23 | 2.33E-05 | 1.61E-03 | Yes |
| FAM213B | 1p36.32 | 2 517 930 | 2 522 908 | 2.93E-09 | 1.14E-06 | rs2843401 | 4.33 | 1.49E-05 | 1.08E-03 | Yes |
| TTC34 | 1p36.32 | 2 567 415 | 2 718 286 | 3.86E-07 | 8.22E-05 | rs2843401 | −5.20 | 1.99E-07 | 1.91E-05 | Yes |
| FCRL3 | 1q23.1 | 157 644 111 | 157 670 647 | 3.47E-06 | 5.31E-04 | rs3761959 | 4.38 | 1.20E-05 | 8.89E-04 | Yes |
| PUS10 | 2p15 | 61 167 357 | 61 245 394 | 2.55E-11 | 1.38E-08 | rs34695944 | 5.31 | 1.10E-07 | 1.11E-05 | Yes |
| AFF3 | 2q11.2 | 100 162 323 | 100 759 201 | 2.92E-07 | 6.51E-05 | rs9653442 | 5.56 | 2.67E-08 | 2.80E-06 | Yes |
| PSD4 | 2q14.1 | 113 914 902 | 113 966 973 | 2.42E-04 | 1.87E-02 | rs3791336 | −3.55 | 3.85E-04 | 2.03E-02 | No |
| PDHB | 3p14.3 | 58 413 357 | 58 419 584 | 3.03E-04 | 2.22E-02 | rs2176082 | −3.50 | 4.71E-04 | 2.39E-02 | Yes |
| FBXO40 | 3q13.33 | 121 311 966 | 121 349 139 | 7.05E-04 | 4.27E-02 | rs4413346 | 3.29 | 1.01E-03 | 4.46E-02 | No |
| DAP | 5p15.2 | 10 679 342 | 10 761 384 | 9.19E-05 | 8.65E-03 | rs267949 | −3.32 | 8.93E-04 | 4.05E-02 | No |
| PPIP5K2 | 5q21.1 | 102 455 853 | 102 548 500 | 3.99E-05 | 4.34E-03 | rs35801 | 3.47 | 5.28E-04 | 2.61E-02 | Yes |
| PAM | 5q21.1 | 102 089 685 | 102 366 809 | 7.33E-09 | 2.64E-06 | rs26258 | −3.35 | 8.11E-04 | 3.70E-02 | Yes |
| IP6K3 | 6p21.31 | 33 689 444 | 33 714 762 | 4.42E-10 | 1.91E-07 | rs2296330 | 6.94 | 3.89E-12 | 5.51E-10 | Yes |
| C6orf106 | 6p21.31 | 34 555 065 | 34 664 636 | 2.14E-06 | 3.49E-04 | rs2814943 | 3.26 | 1.10E-03 | 4.80E-02 | Yes |
| PGBD1 | 6p22.1 | 28 249 314 | 28 270 326 | 3.19E-05 | 3.55E-03 | rs2232428 | −6.47 | 1.00E-10 | 1.26E-08 | No |
| TRIM10 | 6p22.1 | 30 119 722 | 30 128 711 | 7.28E-12 | 6.12E-09 | rs1362126 | 4.38 | 1.20E-05 | 8.89E-04 | No |
| TRIM27 | 6p22.1 | 28 870 779 | 28 891 766 | 1.52E-13 | 4.60E-10 | rs13190937 | −4.12 | 3.79E-05 | 2.51E-03 | No |
| ZNF322 | 6p22.2 | 26 636 518 | 26 659 980 | 7.11E-05 | 7.08E-03 | rs17539358 | 3.74 | 1.85E-04 | 1.07E-02 | No |
| HIST1H2BG | 6p22.2 | 26 216 428 | 26 216 872 | 4.00E-04 | 2.76E-02 | rs17539358 | −3.31 | 9.20E-04 | 4.15E-02 | No |
| IRF5 | 7q32.1 | 128 577 666 | 128 590 089 | 6.43E-13 | 1.22E-09 | rs10488631 | 5.67 | 1.40E-08 | 1.55E-06 | Yes |
| FAM167A | 8p23.1 | 11 278 972 | 11 332 224 | 8.38E-05 | 8.03E-03 | rs13277113 | 4.68 | 2.88E-06 | 2.40E-04 | Yes |
| TRAF1 | 9q33.2 | 123 664 671 | 123 691 451 | 3.95E-05 | 4.34E-03 | rs10818482 | 4.26 | 2.07E-05 | 1.47E-03 | Yes |
| PSMD5 | 9q33.2 | 123 577 774 | 123 605 262 | 1.30E-04 | 1.16E-02 | rs10818482 | 3.75 | 1.75E-04 | 1.02E-02 | Yes |
| PHF19 | 9q33.2 | 123 617 977 | 123 639 606 | 9.31E-08 | 2.35E-05 | rs10818482 | −5.14 | 2.80E-07 | 2.63E-05 | Yes |
| ZNF438 | 10p11.23 | 31 109 136 | 31 320 866 | 7.83E-05 | 7.65E-03 | rs867768 | −3.50 | 4.58E-04 | 2.36E-02 | Yes |
| TMEM258 | 11q12.2 | 61 535 973 | 61 560 274 | 4.94E-04 | 3.24E-02 | rs968567 | −4.77 | 1.87E-06 | 1.59E-04 | Yes |
| FADS1 | 11q12.2 | 61 567 099 | 61 596 790 | 1.08E-04 | 9.77E-03 | rs968567 | −4.55 | 5.30E-06 | 4.20E-04 | Yes |
| DDX6 | 11q23.3 | 118 620 034 | 118 661 858 | 2.01E-07 | 4.62E-05 | rs4938573 | 3.80 | 1.43E-04 | 8.62E-03 | Yes |
| YAF2 | 12q12 | 42 550 906 | 42 632 151 | 6.10E-04 | 3.82E-02 | rs7954523 | 3.30 | 9.70E-04 | 4.35E-02 | No |
| SUOX | 12q13.2 | 56 390 964 | 56 400 425 | 1.10E-07 | 2.70E-05 | rs705699 | 5.39 | 7.02E-08 | 7.18E-06 | Yes |
| RPS26 | 12q13.2 | 56 435 637 | 56 438 116 | 8.40E-08 | 2.18E-05 | rs705699 | −5.06 | 4.17E-07 | 3.87E-05 | Yes |
| METTL21B | 12q14.1 | 58 165 275 | 58 176 324 | 1.03E-05 | 1.34E-03 | rs238516 | −4.40 | 1.06E-05 | 8.08E-04 | Yes |
| TSPAN31 | 12q14.1 | 58 131 796 | 58 143 994 | 3.70E-06 | 5.50E-04 | rs238516 | 4.43 | 9.60E-06 | 7.38E-04 | Yes |
| RNF40 | 16p11.2 | 30 773 066 | 30 787 628 | 6.05E-06 | 8.28E-04 | rs8058578 | 3.86 | 1.13E-04 | 6.91E-03 | No |
| SPNS1 | 16p11.2 | 28 985 542 | 28 995 869 | 1.57E-04 | 1.34E-02 | rs7500321 | 4.15 | 3.25E-05 | 2.21E-03 | No |
| PGAP3 | 17q12 | 37 827 375 | 37 853 050 | 7.72E-07 | 1.52E-04 | rs2872507 | −4.63 | 3.73E-06 | 3.01E-04 | Yes |
| GSDMB | 17q21.1 | 38 060 848 | 38 076 107 | 6.70E-09 | 2.47E-06 | rs2872507 | −5.44 | 5.34E-08 | 5.53E-06 | Yes |
| IKZF3 | 17q21.1 | 37 921 198 | 38 020 441 | 5.59E-06 | 7.76E-04 | rs2872507 | 5.58 | 2.34E-08 | 2.49E-06 | Yes |
| ORMDL3 | 17q21.1 | 38 077 294 | 38 083 854 | 5.87E-08 | 1.64E-05 | rs2872507 | −5.65 | 1.64E-08 | 1.79E-06 | Yes |
| TSSK6 | 19p13.11 | 19 623 227 | 19 626 838 | 4.95E-07 | 1.04E-04 | rs11085264 | 3.76 | 1.70E-04 | 1.00E-02 | No |
| TYK2 | 19p13.2 | 10 461 209 | 10 491 352 | 8.01E-07 | 1.55E-04 | rs2304256 | −6.92 | 4.46E-12 | 6.21E-10 | Yes |
| OPRL1 | 20q13.33 | 62 711 526 | 62 731 996 | 5.97E-04 | 3.75E-02 | rs4408777 | −3.71 | 2.10E-04 | 1.18E-02 | No |
| TMEM50B | 21q22.11 | 34 804 792 | 34 852 318 | 3.06E-04 | 2.23E-02 | rs11702844 | 4.12 | 3.76E-05 | 2.51E-03 | Yes |
| UBASH3A | 21q22.3 | 43 824 008 | 43 867 791 | 2.49E-08 | 7.87E-06 | rs1893592 | −5.73 | 9.81E-09 | 1.10E-06 | Yes |
BP0, start base position; BP1, end base position, hg19/GRCh37 build; CytoBand, cytogenic band where the variant is positioned Top GWAS ID, rsID of the most significant GWAS SNP in locus; Reported, reported genes implicated in previous GWASs.
FUSION, Functional Summary-based Imputation; GWAS, genome-wide association study; RA, rheumatoid arthritis; TWAS, transcriptome-wide association study; UTMOST, unified test for molecular signatures.