Introduction
Materials and methods
Sample collection of synovial tissues and blood
Western blot analysis
Immunohistochemistry
Immunofluorescent labeling
Real-time PCR
Sandwich ELISA detecting serum levels of TXNDC5
ELISA detecting serum levels of anti TXNDC5 antibody
Genomic DNA extraction
SNPs selection
SNP ID | Chromosome position | Locus | Allele | Protein residue | |
---|---|---|---|---|---|
rs1044104 | 7881311 | 3' near gene | C/T | ||
rs9505298 | 7881449 | 3' near gene | A/G | ||
rs41302895 | 7881754 | 3' UTR | A/T | ||
rs1043784 | 7881931 | 3' UTR | A/G | ||
rs7764128 | 7882205 | 3' UTR | A/G | ||
rs8643 | 7883073 | 3' UTR | A/G | ||
rs9502656 | 7883386 | synonymous | T | Asp [D] | |
rs35264740 | 7883865 | intron | C/T | ||
rs17764309 | 7883916 | intron | A/G | ||
rs17696707 | 7884242 | intron | A/G | ||
rs35871461 | 7884291 | intron | C/T | ||
rs2277105 | 7884652 | synonymous | A | Ala [A] | tag SNP |
rs1225936 | 7885184 | intron | A/C | ||
rs1225937 | 7885302 | intron | C/T | ||
rs35794653 | 7885337 | intron | -/A | ||
rs9505300 | 7885364 | intron | C/T | ||
rs1225938 | 7886534 | intron | A/G | ||
rs34342519 | 7886673 | intron | -/C | ||
rs11962800 | 7886905 | intron | A/G | ||
rs9505301 | 7887131 | intron | A/G | ||
rs372578 | 7887223 | intron | A/G | ||
rs7740689 | 7888066 | intron | A/G | ||
rs89715 | 7888168 | intron | C/T | ||
rs7745225 | 7888251 | intron | C/T | ||
rs378963 | 7888328 | intron | C/T | ||
rs45441296 | 7889033 | missense | A | Met [M] | |
rs1225944 | 7889088 | intron | C/T | ||
rs34782746 | 7889254 | intron | C/T | ||
rs1225946 | 7889465 | intron | C/T | ||
rs7746818 | 7889466 | intron | A/G | ||
rs34228534 | 7889773 | frame shift | Gln [Q] | ||
rs1225947 | 7890121 | intron | G/T | ||
rs13873 | 7891160 | intron | G/T | tag SNP | |
rs34963444 | 7891384 | intron | C/T | ||
rs7771314 | 7891403 | intron | C/T | ||
rs9502657 | 7891682 | intron | A/C | ||
rs9502658 | 7891947 | synonymous | T | Phe [F] | |
rs35365768 | 7892037 | intron | -/C | ||
rs1225950 | 7892143 | intron | C/G | ||
rs7749719 | 7894695 | intron | C/T | ||
rs1238994 | 7894794 | intron | G/T | ||
rs35650329 | 7895782 | intron | -/G | ||
rs443861 | 7896491 | intron | A/G | tag SNP | |
rs369086 | 7898875 | intron | A/G | tag SNP | |
rs408014 | 7899394 | intron | A/G | ||
rs368074 | 7899569 | intron | C/G | ||
rs420970 | 7899651 | intron | C/T | ||
rs1225954 | 7900028 | intron | A/G | ||
rs1225955 | 7900709 | intron | A/G | ||
rs6933089 | 7900856 | intron | C/T | ||
rs13209404 | 7909967 | intron | C/T | ||
rs13210097 | 7911345 | 5' near gene | A/C | ||
rs9502663 | 7911474 | 5' near gene | A/C | ||
rs3812162 | 7911702 | 5' near gene | A/C | tag SNP | |
rs34066135 | 7911855 | 5' near gene | -/G | ||
rs1632346 | 7913546 | intron | C/T | tag SNP | |
rs1743634 | 7916207 | intron | A/T | tag SNP | |
rs9505309 | 7917528 | intron | G/T | tag SNP | |
rs6922018 | 7918311 | intron | A/G | tag SNP | |
rs6923488 | 7918405 | intron | C/T | tag SNP | |
rs1594467 | 7920361 | intron | A/G | tag SNP | |
rs419588 | 7920808 | intron | C/T | tag SNP | |
rs365936 | 7920904 | intron | A/C | tag SNP | |
rs1237879 | 7932261 | intron | A/G | tag SNP | |
rs627957 | 7936475 | intron | C/T | tag SNP | |
rs155487 | 7938773 | intron | A/G | tag SNP | |
rs10484327 | 7942566 | intron | A/C | tag SNP | |
rs7764884 | 7970540 | intron | A/G | tag SNP | |
rs7763447 | 7973380 | intron | A/G | tag SNP | |
rs9406071 | 7974705 | intron | C/T | tag SNP | |
rs6597292 | 7975259 | intron | G/T | tag SNP | |
rs197119 | 7976745 | intron | A/G | tag SNP | |
rs6597293 | 7987883 | intron | C/G | tag SNP | |
rs11754300 | 7988766 | intron | C/T | tag SNP | |
rs7744601 | 7988910 | intron | C/T | tag SNP | |
rs2567226 | 7993977 | intron | A/G | tag SNP | |
rs12204273 | 8002705 | intron | A/G | tag SNP | |
rs9392182 | 8009035 | intron | A/T | tag SNP | |
rs2207720 | 8019197 | intron | C/T | tag SNP | |
rs9392189 | 8021532 | intron | A/G | tag SNP | |
rs2815128 | 8023462 | intron | G/T | tag SNP | |
rs2815142 | 8043546 | intron | A/G | tag SNP | |
rs2743992 | 8054722 | intron | A/G | tag SNP | |
rs2294436 | 8057688 | intron | C/T | tag SNP | |
rs2743991 | 8060175 | intron | A/G | tag SNP | |
rs9405369 | 8062437 | intron | A/T | ||
rs12207627 | 8062532 | intron | A/G | ||
rs2743989 | 8064035 | intron | C/T | ||
rs2815153 | 8064050 | intron | C/T | ||
rs2815154 | 8064084 | intron | C/T | ||
rs9328453 | 8065127 | 5' near gene | A/G | ||
rs2815155 | 8065230 | 5' near gene | C/T | ||
rs12660697 | 8065707 | 5' near gene | A/G | ||
rs9392956 | 8065769 | 5' near gene | C/T | ||
rs9392957 | 8065781 | 5' near gene | A/C | ||
rs9505351 | 8066286 | 5' near gene | G/T |
Genotyping using microarray
Genotyping using Taqman SNP assay
Statistical analysis
Results
TXNDC5 expression in the synovial membranes of RA patients
TXNDC5 levels in blood samples from RA patients
Genotyping of SNPs located in TXNDC5
dbSNP identity | Allele/ Genotype | Numbers of patients with RA (%) | Numbers of controls (%) | Fisher's P-value | Odds ratio (95% CI) |
---|---|---|---|---|---|
rs9505298 | A | 75 (0.144) | 10 (0.032) | 1.83E-07 | 5.157303 (2.624041 to 10.136190) |
G | 445 (0.856) | 306 (0.968) | 5.157303 (2.624041 to 10.136190) | ||
AA | 1 (0.004) | 0 (0.000) | 3.13E-07 | ||
AG | 73 (0.281) | 10 (0.063) | |||
GG | 186 (0.715) | 148 (0.937) | |||
rs41302895 | A | 64 (0.120) | 9 (0.028) | 3.32E-06 | 4.725546 (2.317854 to 9.634252) |
T | 468 (0.880) | 311 (0.972) | 4.725546 (2.317854 to 9.634252) | ||
AA | 1 (0.004) | 0 (0.000) | 9.11E-06 | ||
AT | 62 (0.233) | 9 (0.056) | |||
TT | 203 (0.763) | 151 (0.944) | |||
rs1225936 | A | 24 (0.045) | 2 (0.006) | 0.001438 | 7.494071 (1.759029 to 31.927328) |
C | 506 (0.955) | 316 (0.994) | 7.494071 (1.759029 to 31.927328) | ||
AC | 24 (0.091) | 2 (0.013) | 0.001201 | 7.817427 (1.821928 to 33.542572) | |
CC | 241 (0.909) | 157 (0.987) | 7.817427 (1.821928 to 33.542572) | ||
rs1225938 | A | 270 (0.509) | 190 (0.594) | 0.016879 | 0.710526 (0.536647 to 0.940745) |
G | 260 (0.491) | 130 (0.406) | 0.710526 (0.536647 to 0.940745) | ||
AA | 53 (0.200) | 52 (0.325) | 0.013717 | ||
AG | 164 (0.619) | 86 (0.537) | |||
GG | 48 (0.181) | 22 (0.138) | |||
rs372578 | A | 224 (0.424) | 109 (0.341) | 0.015688 | 1.426364 (1.068889 to 1.903392) |
G | 304 (0.576) | 211 (0.659) | 1.426364 (1.068889 to 1.903392) | ||
AA | 45 (0.170) | 21 (0.131) | 0.029497 | ||
AG | 134 (0.508) | 67 (0.419) | |||
GG | 85 (0.322) | 72 (0.450) | |||
rs443861* | A | 117 (0.221) | 48 (0.150) | 0.011538 | 1.605327 (1.109766 to 2.322179) |
G | 413 (0.779) | 272 (0.850) | 1.605327 (1.109766 to 2.322179) | ||
AA | 6 (0.023) | 3 (0.019) | 0.016509 | ||
AG | 105 (0.396) | 42 (0.263) | |||
GG | 154 (0.581) | 115 (0.719) | |||
rs408014 | A | 303 (0.574) | 211 (0.659) | 0.013531 | 0.695671 (0.521353 to 0.928274) |
G | 225 (0.426) | 109 (0.341) | 0.695671 (0.521353 to 0.928274) | ||
AA | 86 (0.326) | 72 (0.450) | 0.03402 | ||
AG | 131 (0.496) | 67 (0.419) | |||
GG | 47 (0.178) | 21 (0.131) | |||
rs9392189* | A | 116 (0.221) | 103 (0.322) | 0.001239 | 0.598991 (0.438317 to 0.818563) |
G | 408 (0.779) | 217 (0.678) | 0.598991 (0.438317 to 0.818563) | ||
AA | 16 (0.061) | 18 (0.113) | 0.007146 | ||
AG | 84 (0.321) | 67 (0.419) | |||
GG | 162 (0.618) | 75 (0.469) | |||
rs2743992* | A | 230 (0.437) | 163 (0.509) | 0.041455 | 0.748425 (0.566338 to 0.989055) |
G | 296 (0.563) | 157 (0.491) | 0.748425 (0.566338 to 0.989055) | ||
AA | 43 (0.163) | 44 (0.275) | 0.022536 | ||
AG | 144 (0.548) | 75 (0.469) | |||
GG | 76 (0.289) | 41 (0.256) |
dbSNP identity | Allele/Genotype | Numbers of patients with RA (%) | Numbers of controls (%) | Fisher's P-value | Odds Ratio (95% CI) |
---|---|---|---|---|---|
rs1044104 | A | 49 (0.480) | 103 (0.322) | 0.0037 | 1.947793 (.237327 to 3.066204) |
G | 53 (0.520) | 217 (0.678) | 1.947793 (.237327 to 3.066204) | ||
AA | 13 (0.255) | 20 (0.125) | 0.022555 | ||
AG | 23 (0.451) | 63 (0.394) | |||
GG | 15 (0.294) | 77 (0.481) | |||
rs1225937 | A | 67 (0.657) | 252 (0.787) | 0.007503 | 0.516553 (0.316863 to 0.842090) |
G | 35 (0.343) | 68 (0.212) | 0.516553 (0.316863 to 0.842090) | ||
AA | 22 (0.431) | 99 (0.619) | 0.027945 | ||
AG | 23 (0.451) | 54 (0.338) | |||
GG | 6 (0.118) | 7 (0.044) | |||
rs1225938 | A | 46 (0.451) | 190 (0.594) | 0.011468 | 0.562030 (0.358612 to 0.880834) |
G | 56 (0.549) | 130 (0.406) | 0.562030 (0.358612 to 0.880834) | ||
AA | 11 (0.216) | 52 (0.325) | 0.013973 | ||
AG | 24 (0.471) | 86 (0.537) | |||
GG | 16 (0.314) | 22 (0.138) | |||
rs372578 | A | 50 (0.490) | 109 (0.341) | 0.006659 | 1.861327 (1.184652 to 2.924518) |
G | 52 (0.510) | 211 (0.659) | 1.861327 (1.184652 to 2.924518) | ||
AA | 14 (0.275) | 21 (0.131) | 0.029107 | ||
AG | 22 (0.431) | 67 (0.419) | |||
GG | 15 (0.294) | 72 (0.450) | |||
rs89715 | A | 52 (0.510) | 212 (0.662) | 0.005544 | 0.529811 (0.337112 to 0.832662) |
G | 50 (0.490) | 108 (0.338) | 0.529811 (0.337112 to 0.832662) | ||
AA | 15 (0.294) | 73 (0.456) | 0.026647 | ||
AG | 22 (0.431) | 66 (0.412) | |||
GG | 14 (0.275) | 21 (0.131) | |||
rs378963 | A | 63 (0.643) | 253 (0.791) | 0.002897 | 0.476680 (0.291090 to 0.780596) |
G | 35 (0.357) | 67 (0.209) | 0.476680 (0.291090 to 0.780596) | ||
AA | 20 (0.408) | 100 (0.625) | 0.012477 | ||
AG | 23 (0.469) | 53 (0.331) | |||
GG | 6 (0.122) | 7 (0.044) | |||
rs1225944 | A | 35 (0.357) | 66 (0.206) | 0.002276 | 2.138047 (1.304553 to 3.504071) |
G | 63 (0.643) | 254 (0.794) | 2.138047 (1.304553 to 3.504071) | ||
AA | 6 (0.122) | 7 (0.044) | 0.010406 | ||
AG | 23 (0.469) | 52 (0.325) | |||
GG | 20 (0.408) | 101 (0.631) | |||
rs1225947 | A | 51 (0.500) | 108 (0.338) | 0.0032 | 1.962963 (1.249087 to 3.084832) |
C | 51 (0.500) | 212 (0.662) | 1.962963 (1.249087 to 3.084832) | ||
AA | 13 (0.255) | 21 (0.131) | 0.017854 | ||
AC | 25 (0.490) | 66 (0.412) | |||
CC | 13 (0.255) | 73 (0.456) | |||
rs1238994 | A | 52 (0.510) | 210 (0.656) | 0.007966 | 0.544762 (0.346807 to 0.855709) |
C | 50 (0.490) | 110 (0.344) | 0.544762 (0.346807 to 0.855709) | ||
AA | 15 (0.294) | 71 (0.444) | 0.031615 | ||
AC | 22 (0.431) | 68 (0.425) | |||
CC | 14 (0.275) | 21 (0.131) | |||
rs369086* | A | 35 (0.343) | 66 (0.208) | 0.005322 | 1.994573 (1.221370 to 3.257261) |
G | 67 (0.657) | 252 (0.792) | 1.994573 (1.221370 to 3.257261) | ||
AA | 6 (0.118) | 7 (0.044) | 0.022037 | ||
AG | 23 (0.451) | 52 (0.327) | |||
GG | 22 (0.431) | 100 (0.629) | |||
rs408014 | A | 50 (0.500) | 211 (0.659) | 0.004146 | 0.516588 (0.327716 to 0.814312) |
G | 50 (0.500) | 109 (0.341) | 0.516588 (0.327716 to 0.814312) | ||
AA | 14 (0.280) | 72 (0.450) | 0.020441 | ||
AG | 22 (0.440) | 67 (0.419) | |||
GG | 14 (0.280) | 21 (0.131) | |||
rs368074 | C | 50 (0.500) | 109 (0.341) | 0.004146 | 1.935780 (1.228031 to 3.051425) |
G | 50 (0.500) | 211 (0.659) | 1.935780 (1.228031 to 3.051425) | ||
CC | 14 (0.280) | 21 (0.131) | 0.020441 | ||
CG | 22 (0.440) | 67 (0.419) | |||
GG | 14 (0.280) | 72 (0.450) | |||
rs1225954 | A | 50 (0.500) | 109 (0.341) | 0.004146 | 1.935780 (1.228031 to 3.051425) |
G | 50 (0.500) | 11 (0.659) | 1.935780 (1.228031 to 3.051425) | ||
AA | 14 (0.280) | 21 (0.131) | 0.020441 | ||
AG | 22 (0.440) | 67 (0.419) | |||
GG | 14 (0.280) | 72 (0.450) | |||
rs1225955 | A | 50 (0.500) | 108 (0.338) | 0.003427 | 1.962963 (1.244946 to 3.095092) |
G | 50 (0.500) | 212 (0.662) | 1.962963 (1.244946 to 3.095092) | ||
AA | 14 (0.280) | 21 (0.131) | 0.018534 | ||
AG | 22 (0.440) | 66 (0.412) | |||
GG | 14 (0.280) | 73 (0.456) | |||
rs13209404 | A | 30 (0.300) | 59 (0.184) | 0.013556 | 1.895884 (1.135508 to 3.165434) |
G | 70 (0.700) | 261 (0.816) | 1.895884 (1.135508 to 3.165434) | ||
AA | 4 (0.080) | 7 (0.044) | 0.043599 | ||
AG | 22 (0.440) | 45 (0.281) | |||
GG | 24 (0.480) | 108 (0.675) | |||
rs3812162* | A | 70 (0.700) | 268 (0.838) | 0.002475 | 0.452736 (0.268969 to 0.762060) |
C | 30 (0.300) | 52 (0.163) | 0.452736 (0.268969 to 0.762060) | ||
AA | 23 (0.460) | 114 (0.713) | 0.004576 | ||
AC | 24 (0.480) | 40 (0.250) | |||
CC | 3 (0.060) | 6 (0.037) |
Haplotype | Freq. | Case, Control Ratio Counts | Case, Control Frequencies | P-Value |
---|---|---|---|---|
Block 1 | ||||
AGG | 0.827 | 426.9: 101.1, 273.0: 45.0 | 0.808, 0.858 | 0.0625 |
GAA | 0.145 | 81.0: 447.0, 42.0: 276.0 | 0.153, 0.132 | 0.3939 |
AAG | 0.012 | 7.8: 520.2, 2.0: 316.0 | 0.015, 0.006 | 0.2649 |
Block 2
| ||||
AA | 0.814 | 418.9: 109.1, 269.9: 48.1 | 0.793, 0.849 | 0.0446 |
GG | 0.155 | 87.9: 440.1, 42.9: 275.1 | 0.166, 0.135 | 0.2187 |
AG | 0.024 | 15.1: 512.9, 5.1: 312.9 | 0.029, 0.016 | 0.2441 |
Block 3
| ||||
GAAG | 0.597 | 297.7: 230.3, 207.0: 111.0 | 0.564, 0.651 | 0.0125 |
AGGA | 0.236 | 135.3: 392.7, 64.0: 254.0 | 0.256, 0.201 | 0.0674 |
AGAG | 0.146 | 83.8: 444.2, 40.0: 278.0 | 0.159, 0.126 | 0.1902 |
AAAG | 0.012 | 6.1: 521.9, 4.0: 314.0 | 0.012, 0.013 | 0.8831 |
Block 4
| ||||
GAGGGGA | 0.6 | 296.8: 227.2, 207.0: 109.0 | 0.566, 0.655 | 0.0112 |
AGCAAAC | 0.202 | 120.9: 403.1, 49.0: 267.0 | 0.231, 0.155 | 0.0081 |
GGCAAGA | 0.149 | 83.0: 441.0, 42.0: 274.0 | 0.158, 0.133 | 0.3157 |
AGCAAGA | 0.022 | 10.1: 513.9, 8.0: 308.0 | 0.019, 0.025 | 0.5599 |
AGCAAAA | 0.017 | 6.0: 518.0, 8.0: 308.0 | 0.012, 0.025 | 0.1299 |
Block 5
| ||||
GG | 0.669 | 344.6: 183.4, 220.9: 97.1 | 0.653, 0.695 | 0.2075 |
AA | 0.213 | 112.6: 415.4, 67.6: 250.4 | 0.213, 0.213 | 0.9829 |
AG | 0.117 | 69.7: 458.3, 29.4: 288.6 | 0.132, 0.092 | 0.0828 |
Block 6
| ||||
AA | 0.715 | 380.5: 145.5, 222.8: 95.2 | 0.723, 0.701 | 0.4774 |
AG | 0.18 | 88.7: 437.3, 63.5: 254.5 | 0.169, 0.200 | 0.2564 |
GG | 0.1 | 53.3: 472.7, 31.5: 286.5 | 0.101, 0.099 | 0.9173 |
Block 7
| ||||
AA | 0.699 | 374.8: 153.2, 216.9: 101.1 | 0.710, 0.682 | 0.3934 |
AG | 0.214 | 110.9: 417.1, 70.1: 247.9 | 0.210, 0.220 | 0.7211 |
GG | 0.085 | 41.1: 486.9, 30.9: 287.1 | 0.078, 0.097 | 0.3288 |
Block 8
| ||||
AG | 0.531 | 294.0: 232.0, 153.8: 164.2 | 0.559, 0.484 | 0.0336 |
AA | 0.376 | 187.8: 338.2, 129.2: 188.8 | 0.357, 0.406 | 0.1518 |
GA | 0.092 | 42.9: 483.1, 34.8: 283.2 | 0.082, 0.109 | 0.1742 |
Haplotype | Freq. | Case, control ratio counts | Case, control frequencies | P-value |
---|---|---|---|---|
Block 1 | ||||
AGGG | 0.755 | 75.0: 27.0, 242.0: 76.0 | 0.735, 0.761 | 0.5994 |
GAAA | 0.136 | 15.0: 87.0, 42.0: 276.0 | 0.147, 0.132 | 0.7006 |
AAGG | 0.1 | 11.0: 91.0, 31.0: 287.0 | 0.108, 0.097 | 0.7616 |
Block 2
| ||||
AAAGAAG | 0.541 | 45.0: 57.0, 182.2: 135.8 | 0.441, 0.573 | 0.0198 |
GAAAGGA | 0.23 | 34.0: 68.0, 62.5: 255.5 | 0.333, 0.196 | 0.0043 |
GGGAGAG | 0.126 | 13.0: 89.0, 40.0: 278.0 | 0.127, 0.126 | 0.9686 |
GAAGAAG | 0.065 | 6.0: 96.0, 21.3: 296.7 | 0.059, 0.067 | 0.7731 |
Block 3
| ||||
AGGAGGGGA | 0.609 | 49.7: 51.9, 206.0: 112.0 | 0.489, 0.648 | 0.0044 |
CGAGCAAAC | 0.187 | 29.8: 71.8, 49.0: 269.0 | 0.293, 0.154 | 0.0018 |
CAGGCAAGA | 0.134 | 14.3: 87.3, 42.0: 276.0 | 0.140, 0.132 | 0.829 |
CGAGCAAAA | 0.022 | 1.2: 100.4, 8.0: 310.0 | 0.012, 0.025 | 0.4324 |
CGAGCAAGA | 0.017 | 4.0: 97.6, 3.0: 315.0 | 0.039, 0.010 | 0.0408 |
CAAGCAAGA | 0.012 | 0.0: 101.6, 5.0: 313.0 | 0.000, 0.016 | 0.2042 |
Block 4
| ||||
GG | 0.664 | 58.0: 44.0, 221.0: 97.0 | 0.569, 0.695 | 0.0187 |
AA | 0.228 | 28.0: 74.0, 67.7: 250.3 | 0.275, 0.213 | 0.1962 |
AG | 0.108 | 16.0: 86.0, 29.3: 288.7 | 0.157, 0.092 | 0.067 |
Block 5
| ||||
AAA | 0.523 | 45.9: 56.1, 173.7: 144.3 | 0.450, 0.546 | 0.0915 |
AGC | 0.29 | 33.3: 68.7, 88.6: 229.4 | 0.327, 0.279 | 0.3548 |
GGC | 0.097 | 7.6: 94.4, 33.0: 285.0 | 0.075, 0.104 | 0.3851 |
AAC | 0.072 | 10.7: 91.3, 19.4: 298.6 | 0.105, 0.061 | 0.1339 |
AGA | 0.013 | 4.1: 97.9, 1.3: 316.7 | 0.040, 0.004 | 0.0053 |
Block 6
| ||||
AAA | 0.709 | 77.9: 24.1, 219.8: 98.2 | 0.764, 0.691 | 0.159 |
AGG | 0.101 | 9.5: 92.5, 32.9: 285.1 | 0.093, 0.104 | 0.7639 |
GGG | 0.096 | 9.4: 92.6, 30.9: 287.1 | 0.092, 0.097 | 0.8872 |
AGA | 0.084 | 5.0: 97.0, 30.1: 287.9 | 0.049, 0.095 | 0.1475 |
Block 7
| ||||
AA | 0.683 | 70.0: 32.0, 217.0: 101.0 | 0.686, 0.682 | 0.9415 |
AG | 0.221 | 23.0: 79.0, 70.0: 248.0 | 0.225, 0.220 | 0.9096 |
GG | 0.095 | 9.0: 93.0, 31.0: 287.0 | 0.088, 0.097 | 0.7819 |
Block 8
| ||||
GAAGA | 0.49 | 53.9: 48.1, 151.8: 166.2 | 0.529, 0.477 | 0.3656 |
GAAAA | 0.198 | 21.1: 80.9, 62.1: 255.9 | 0.206, 0.195 | 0.8077 |
AAAAG | 0.14 | 14.0: 88.0, 44.9: 273.1 | 0.137, 0.141 | 0.9123 |
AAAAA | 0.059 | 3.0: 99.0, 22.0: 296.0 | 0.029, 0.069 | 0.14 |
ACGAA | 0.057 | 5.0: 97.0, 19.0: 299.0 | 0.049, 0.060 | 0.6831 |
AAGAA | 0.042 | 4.0: 98.0, 13.9: 304.1 | 0.039, 0.044 | 0.8369 |
Block 9
| ||||
AT | 0.517 | 53.0: 49.0, 164.0: 154.0 | 0.520, 0.516 | 0.9455 |
GA | 0.28 | 26.6: 75.4, 91.0: 227.0 | 0.261, 0.286 | 0.6165 |
GT | 0.203 | 22.4: 79.6, 63.0: 255.0 | 0.220, 0.198 | 0.6357 |
Block 10
| ||||
AG | 0.802 | 78.2: 23.8, 258.5: 59.5 | 0.767, 0.813 | 0.3066 |
GA | 0.161 | 18.7: 83.3, 48.8: 269.2 | 0.184, 0.153 | 0.4683 |
GG | 0.032 | 3.8: 98.2, 9.5: 308.5 | 0.037, 0.030 | 0.7032 |
dbSNP identity | Allele/ Genotype | No. of patients with RA (%) | No. of controls (%) | Fisher's P-value |
---|---|---|---|---|
rs2277105 | C | 1581 (0.840) | 1512 (0.848) | 0.491098 |
O(freq) | 19 (0.010) | 12 (0.007) | ||
T | 283 (0.150) | 260 (0.146) | ||
CC | 670 (0.719) | 650 (0.734) | 0.549842 | |
CT | 241 (0.259) | 212 (0.239) | ||
TT | 21 (0.023) | 24 (0.027) | ||
rs11962800 | A | 1568 (0.831) | 1523 (0.853) | 0.173781 |
O(freq) | 15 (0.008) | 11 (0.006) | ||
G | 304 (0.161) | 251 (0.141) | ||
AA | 656 (0.701) | 656 (0.740) | 0.184145 | |
AG | 256 (0.274) | 211 (0.238) | ||
GG | 24 (0.026) | 20 (0.023) | ||
rs443861 | A | 357 (0.190) | 275 (0.154) | 0.00832 |
O(freq) | 19 (0.010) | 12 (0.007) | ||
G | 1507 (0.800) | 1497 (0.839) | ||
AA | 51 (0.055) | 26 (0.029) | 0.01011 | |
AG | 255 (0.274) | 223 (0.252) | ||
GG | 626 (0.672) | 637 (0.719) | ||
rs369086 | A | 485 (0.257) | 460 (0.258) | 0.510123 |
O(freq) | 18 (0.010) | 11 (0.006) | ||
G | 1381 (0.733) | 1314 (0.736) | ||
AA | 61 (0.065) | 71 (0.080) | 0.260584 | |
AG | 363 (0.389) | 318 (0.359) | ||
GG | 509 (0.546) | 498 (0.561) |