| Literature DB >> 21801346 |
Xiaotian Chang1, Yan Zhao, Xinfeng Yan, Jihong Pan, Kehua Fang, Lin Wang.
Abstract
INTRODUCTION: Expression of TXNDC5, which is induced by hypoxia, stimulates cell proliferation and angiogenesis. Our previous study detected increased TXNDC5 expression in the synovial tissues of rheumatoid arthritis (RA) patients using proteomic methods. The current study investigated a pathogenic role for TXNDC5 in RA.Entities:
Mesh:
Substances:
Year: 2011 PMID: 21801346 PMCID: PMC3239364 DOI: 10.1186/ar3429
Source DB: PubMed Journal: Arthritis Res Ther ISSN: 1478-6354 Impact factor: 5.156
Single nucleotide polymorphism (SNP) information
| SNP ID | Chromosome | 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 |
Figure 1Immunodetection of TXNDC5 in synovial membranes from patients with RA, OA and AS. (A) Immunolocalization of TXNDC5 in synovial membranes. The left lane indicates results of immunohistochemistry, and the right lane indicates results of immunofluorescent labeling. Original magnification: 100×. Arrows indicate the upper layer of synovial membranes. (B) Semi-quantitative analysis of immunofluorescent signals of TXNDC5. TXNDC5 had significantly higher expression in the synovial tissue of RA patients compared to the synovial tissues of OA and AS patients. AS, ankylosing spondylitis; OA, osteoarthritis; RA, rheumatoid arthritis.
Figure 2Quantitative analysis of TXNDC5 expression. (A) TXNDC5 at molecular weight of 50 kDa was detected in synovial tissues of RA, OA and AS patients using Western blot analysis. Sample loading was normalized using GADPH at molecular weight of 37 kDa. (B) TXNDC5 expression was semi-quantitatively analyzed by normalizing the signal density of TXNDC5 to that of GADPH. (C) TXNDC5 mRNA expression was measured in synovial tissues using real time PCR. The expression was normalized to that of β-actin. TXNDC5 had significantly higher expression in the synovial tissue of RA patients compared to the synovial tissues of OA and AS patients. AS, ankylosing spondylitis; OA, osteoarthritis; RA, rheumatoid arthritis.
Figure 3Serum levels of TXNDC5 and anti-TXNDC5 antibody in patients with arthritic diseases and healthy controls. TXNDC5 levels are represented by OD values of absorbance at 405 nm and are expressed as the mean ± standard error of the mean. (A) A sandwich ELISA detected increased level of TXNDC5 in blood samples from RA patients compared to samples from OA, AS and SLE patients, as well as from healthy controls. (B) An ELISA indicated that levels of anti-TXNDC5 antibodies were not significantly different among blood samples from RA, OA and AS patients and the healthy controls. AS, ankylosing spondylitis; OA, osteoarthritis; RA, rheumatoid arthritis.
Allele and genotype frequencies in a case-control cohort of patients with RA
| dbSNP identity | Allele/ | Numbers of patients | Numbers of controls (%) | Fisher's | 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) |
160 controls and 266 cases were observed; *represents tag SNP
95% CI, 95% confidence interval; RA, rheumatoid arthritis; SNP, single nucleotide polymorphism
Allele and genotype frequencies in a case-control cohort of patients with AS
| dbSNP identity | Allele/Genotype | Numbers of patients with RA (%) | Numbers of controls (%) | Fisher's | 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) |
160 controls & 266 cases were observed; *represents tag SNP. 95% CI, 95% confidence interval; AS, ankylosing spondylitis; SNP, single nucleotide polymorphism.
Figure 4LD plot of the 96 genotyped SNPs in the TXNDC5 gene. (A) Linkage disequilibrium in the RA group. (B) Linkage disequilibrium in the AS group. Red areas representing higher levels of LD. Blue areas represent LD comparisons with low confidence of estimation. Dark triangles represent haplotype blocks. Numbers in squares are D' values. AS, ankylosing spondylitis; RA, rheumatoid arthritis; SNP, single nucleotide polymorphism.
Haplotype frequencies in a case-control cohort of patients with rheumatoid arthritis
| Haplotype | Case, Control Ratio Counts | Case, Control Frequencies | ||
|---|---|---|---|---|
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 frequencies in a case-control cohort of patients with ankylosing spondylitis
| Haplotype | Case, control ratio counts | Case, control frequencies | ||
|---|---|---|---|---|
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
Allele and genotype frequencies in a case-control cohort of patients with RA
| dbSNP identity | Allele/ | No. of patients with RA (%) | No. of controls (%) | Fisher's |
|---|---|---|---|---|
| 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) |
898 controls and 951 RA cases observed. RA, rheumatoid arthritis; SNP, single nucleotide polymorphism