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Table 6 The specific haplotypes and the phenotype “MTX-nausea”

From: Single nucleotide polymorphisms associated with methotrexate-induced nausea in juvenile idiopathic arthritis

Chr Markers Haplotype F cases F controls Score p-value p-sim
1 rs1801131-rs1801133 A-C 0.321 0.405 −1.067 0.286 0.333
1 rs1801131-rs1801133 A-T 0.304 0.286 0.222 0.825 0.837
1 rs1801131-rs1801133 C-C 0.376 0.310 0.730 0.465 0.523
1 rs1801131-rs1801133 C-T 0.000 0.000 NA NA NA
7 rs1045642-rs2032582 C-A 0.027 0.048 NA NA NA
7 rs1045642-rs2032582 C-G 0.420 0.405 0.184 0.854 0.929
7 rs1045642-rs2032582 C-T 0.000 0.000 NA NA NA
7 rs1045642-rs2032582 T-G 0.152 0.143 0.144 0.886 0.917
7 rs1045642-rs2032582 T-T 0.402 0.405 −0.035 0.972 0.931
10 rs717620-rs2273697-rs3740066 A-A-A 0.000 NA NA NA NA
10 rs717620-rs2273697-rs3740066 A-A-G 0.214 0.214 0.000 1.000 0.964
10 rs717620-rs2273697-rs3740066 A-G-A 0.000 NA NA NA NA
10 rs717620-rs2273697-rs3740066 G-A-A 0.014 0.000 NA NA NA
10 rs717620-rs2273697-rs3740066 G-A-G 0.272 0.214 0.735 0.463 0.478
10 rs717620-rs2273697-rs3740066 G-G-A 0.159 0.167 −0.011 0.991 0.977
10 rs717620-rs2273697-rs3740066 G-G-G 0.341 0.405 −0.802 0.423 0.385
10 rs717620-rs2273697 A-A 0.000 0.000 NA NA NA
10 rs717620-rs2273697 A-G 0.214 0.214 0.000 1.000 0.94
10 rs717620-rs2273697 G-A 0.286 0.214 0.783 0.434 0.44
10 rs717620-rs2273697 G-G 0.500 0.571 −0.748 0.454 0.469
10 rs2273697-rs3740066 A-A 0.013 0.000 NA NA NA
10 rs2273697-rs3740066 A-G 0.273 0.214 0.706 0.480 0.534
10 rs2273697-rs3740066 G-A 0.376 0.381 −0.014 0.989 0.966
10 rs2273697-rs3740066 G-G 0.338 0.405 −0.791 0.429 0.397
11 rs1176744-rs1062613-rs1985242-rs1176713 G-C-A-C 0.070 0.035 0.589 0.556 0.552
11 rs1176744-rs1062613-rs1985242-rs1176713 G-C-T-T 0.030 NA NA NA NA
11 rs1176744-rs1062613-rs1985242-rs1176713 G-T-A-T 0.144 0.288 −1.331 0.183 0.171
11 rs1176744-rs1062613-rs1985242-rs1176713 T-C-A-C 0.060 NA 1.641 0.101 0.076
11 rs1176744-rs1062613-rs1985242-rs1176713 T-C-T-T 0.026 0.010 NA NA NA
11 rs1176744-rs1062613-rs1985242-rs1176713 T-T-A-C 0.035 0.064 −0.373 0.709 0.78
11 rs1176744-rs1062613-rs1985242-rs1176713 T-T-A-T 0.000 0.024 NA NA NA
11 rs1176744-rs1062613-rs1985242 G-C-A NA 0.000 NA NA NA
11 rs1176744-rs1062613-rs1985242 G-C-T 0.534 0.470 0.151 0.880 0.87
11 rs1176744-rs1062613-rs1985242 G-T-A 0.059 0.020 0.943 0.346 0.38
11 rs1176744-rs1062613-rs1985242 T-C-A 0.042 0.060 0.086 0.931 0.917
11 rs1176744-rs1062613-rs1985242 T-C-T NA 0.0282 NA NA NA
11 rs1176744-rs1062613-rs1985242 T-T-A 0.098 0.034 1.044 0.297 0.281
11 rs1176744-rs1062613-rs1985242 T-T-T 0.144 0.299 −1.300 0.194 0.197
11 rs1062613-rs1985242-rs1176713 C-A-C 0.089 0.000 1.273 0.203 0.234
11 rs1062613-rs1985242-rs1176713 C-T-C 0.036 0.089 −0.798 0.425 0.455
11 rs1062613-rs1985242-rs1176713 C-T-T 0.535 0.459 0.128 0.898 0.898
11 rs1062613-rs1985242-rs1176713 T-A-C 0.099 0.091 0.893 0.372 0.4
11 rs1062613-rs1985242-rs1176713 T-A-T NA 0.028 NA NA NA
11 rs1062613-rs1985242-rs1176713 T-T-T 0.104 0.099 0.184 0.854 0.864
11 rs1176744-rs1062613 G-C 0.030 0.025 NA NA NA
11 rs1176744-rs1062613 G-T NA 0.000 NA NA NA
11 rs1176744-rs1062613 T-C 0.679 0.757 −1.075 0.282 0.255
11 rs1176744-rs1062613 T-T 0.119 0.020 1.760 0.078 0.09
11 rs1062613-rs1985242 C-A 0.068 0.070 −0.053 0.958 0.997
11 rs1062613-rs1985242 C-T 0.000 0.028 NA NA NA
11 rs1062613-rs1985242 T-A 0.252 0.333 −0.579 0.563 0.564
11 rs1062613-rs1985242 T-T 0.078 0.000 1.293 0.196 0.162
11 rs1985242-rs1176713 A-C 0.560 0.548 −0.264 0.792 0.802
11 rs1985242-rs1176713 A-T 0.109 0.119 0.494 0.621 0.592
11 rs1985242-rs1176713 T-C 0.134 0.124 0.256 0.798 0.826
11 rs1985242-rs1176713 T-T 0.679 0.757 −1.072 0.284 0.241
12 rs2117032-rs4149056-rs4149081 C-C-A 0.105 0.000 1.143 0.253 0.26
12 rs2117032-rs4149056-rs4149081 C-C-G 0.279 0.333 0.009 0.993 0.978
12 rs2117032-rs4149056-rs4149081 C-T-G 0.056 0.143 −0.827 0.408 0.419
12 rs2117032-rs4149056-rs4149081 T-C-A 0.009 0.024 NA NA NA
12 rs2117032-rs4149056-rs4149081 T-T-G 0.551 0.500 −0.041 0.968 0.968
12 rs2117032-rs4149056 C-C 0.105 0.000 1.135 0.256 0.257
12 rs2117032-rs4149056 C-T 0.279 0.333 0.011 0.991 0.96
12 rs2117032-rs4149056 T-C 0.056 0.143 −0.824 0.410 0.5
12 rs2117032-rs4149056 T-T 0.560 0.524 −0.200 0.841 0.843
12 rs4149056-rs4149081 C-A 0.161 0.143 0.285 0.776 0.617
12 rs4149056-rs4149081 C-G 0.009 0.024 NA NA NA
12 rs4149056-rs4149081 T-G 0.830 0.833 −0.047 0.963 0.869
  1. The haplotype-specific scores for the listed markers in association with the child-assessed MTX-induced nausea – the nausea diary
  2. N = 77, the patients who had completed at least seven diary entries
  3. Chr; Chromosome. Markers; the SNPs in the haplotype. Haplotypes; the alleles for the SNPs in the haplotype. Cases; MTXnausea (n = 56). Controls (n = 21). Fcases; Frequency of the haplotype among cases, Fcontrols, Frequency of the haplotype among controls. Score; the haplotype association test score for the specific haplotype. P-sim; the number of times the simulated score statistics exceeds the observed divided by the total number of simulations (1000)
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