Table 1

The significant genes for RA risk in both cross-tissue and single-tissue TWAS analysis

GeneCytoBandBP0BP1UTMOST_DiscoveryFUSION_ReplicationReported
PUTMOSTPFDRTop GWAS IDZ scorePFUSIONPFDR
PTPN221p13.2114 356 433114 414 3811.82E-111.19E-08rs24766016.751.51E-112.03E-09Yes
INPP5B1p34.338 326 36938 412 7291.24E-095.06E-07rs284113524.986.29E-075.77E-05Yes
ATP13A21p36.1317 312 45317 338 4232.84E-042.13E-02rs22403353.811.39E-048.44E-03Yes
MMEL11p36.322 522 0782 564 4811.04E-083.57E-06rs28434014.232.33E-051.61E-03Yes
FAM213B1p36.322 517 9302 522 9082.93E-091.14E-06rs28434014.331.49E-051.08E-03Yes
TTC341p36.322 567 4152 718 2863.86E-078.22E-05rs2843401−5.201.99E-071.91E-05Yes
FCRL31q23.1157 644 111157 670 6473.47E-065.31E-04rs37619594.381.20E-058.89E-04Yes
PUS102p1561 167 35761 245 3942.55E-111.38E-08rs346959445.311.10E-071.11E-05Yes
AFF32q11.2100 162 323100 759 2012.92E-076.51E-05rs96534425.562.67E-082.80E-06Yes
PSD42q14.1113 914 902113 966 9732.42E-041.87E-02rs3791336−3.553.85E-042.03E-02No
PDHB3p14.358 413 35758 419 5843.03E-042.22E-02rs2176082−3.504.71E-042.39E-02Yes
FBXO403q13.33121 311 966121 349 1397.05E-044.27E-02rs44133463.291.01E-034.46E-02No
DAP5p15.210 679 34210 761 3849.19E-058.65E-03rs267949−3.328.93E-044.05E-02No
PPIP5K25q21.1102 455 853102 548 5003.99E-054.34E-03rs358013.475.28E-042.61E-02Yes
PAM5q21.1102 089 685102 366 8097.33E-092.64E-06rs26258−3.358.11E-043.70E-02Yes
IP6K36p21.3133 689 44433 714 7624.42E-101.91E-07rs22963306.943.89E-125.51E-10Yes
C6orf1066p21.3134 555 06534 664 6362.14E-063.49E-04rs28149433.261.10E-034.80E-02Yes
PGBD16p22.128 249 31428 270 3263.19E-053.55E-03rs2232428−6.471.00E-101.26E-08No
TRIM106p22.130 119 72230 128 7117.28E-126.12E-09rs13621264.381.20E-058.89E-04No
TRIM276p22.128 870 77928 891 7661.52E-134.60E-10rs13190937−4.123.79E-052.51E-03No
ZNF3226p22.226 636 51826 659 9807.11E-057.08E-03rs175393583.741.85E-041.07E-02No
HIST1H2BG6p22.226 216 42826 216 8724.00E-042.76E-02rs17539358−3.319.20E-044.15E-02No
IRF57q32.1128 577 666128 590 0896.43E-131.22E-09rs104886315.671.40E-081.55E-06Yes
FAM167A8p23.111 278 97211 332 2248.38E-058.03E-03rs132771134.682.88E-062.40E-04Yes
TRAF19q33.2123 664 671123 691 4513.95E-054.34E-03rs108184824.262.07E-051.47E-03Yes
PSMD59q33.2123 577 774123 605 2621.30E-041.16E-02rs108184823.751.75E-041.02E-02Yes
PHF199q33.2123 617 977123 639 6069.31E-082.35E-05rs10818482−5.142.80E-072.63E-05Yes
ZNF43810p11.2331 109 13631 320 8667.83E-057.65E-03rs867768−3.504.58E-042.36E-02Yes
TMEM25811q12.261 535 97361 560 2744.94E-043.24E-02rs968567−4.771.87E-061.59E-04Yes
FADS111q12.261 567 09961 596 7901.08E-049.77E-03rs968567−4.555.30E-064.20E-04Yes
DDX611q23.3118 620 034118 661 8582.01E-074.62E-05rs49385733.801.43E-048.62E-03Yes
YAF212q1242 550 90642 632 1516.10E-043.82E-02rs79545233.309.70E-044.35E-02No
SUOX12q13.256 390 96456 400 4251.10E-072.70E-05rs7056995.397.02E-087.18E-06Yes
RPS2612q13.256 435 63756 438 1168.40E-082.18E-05rs705699−5.064.17E-073.87E-05Yes
METTL21B12q14.158 165 27558 176 3241.03E-051.34E-03rs238516−4.401.06E-058.08E-04Yes
TSPAN3112q14.158 131 79658 143 9943.70E-065.50E-04rs2385164.439.60E-067.38E-04Yes
RNF4016p11.230 773 06630 787 6286.05E-068.28E-04rs80585783.861.13E-046.91E-03No
SPNS116p11.228 985 54228 995 8691.57E-041.34E-02rs75003214.153.25E-052.21E-03No
PGAP317q1237 827 37537 853 0507.72E-071.52E-04rs2872507−4.633.73E-063.01E-04Yes
GSDMB17q21.138 060 84838 076 1076.70E-092.47E-06rs2872507−5.445.34E-085.53E-06Yes
IKZF317q21.137 921 19838 020 4415.59E-067.76E-04rs28725075.582.34E-082.49E-06Yes
ORMDL317q21.138 077 29438 083 8545.87E-081.64E-05rs2872507−5.651.64E-081.79E-06Yes
TSSK619p13.1119 623 22719 626 8384.95E-071.04E-04rs110852643.761.70E-041.00E-02No
TYK219p13.210 461 20910 491 3528.01E-071.55E-04rs2304256−6.924.46E-126.21E-10Yes
OPRL120q13.3362 711 52662 731 9965.97E-043.75E-02rs4408777−3.712.10E-041.18E-02No
TMEM50B21q22.1134 804 79234 852 3183.06E-042.23E-02rs117028444.123.76E-052.51E-03Yes
UBASH3A21q22.343 824 00843 867 7912.49E-087.87E-06rs1893592−5.739.81E-091.10E-06Yes
  • 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.