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Table 5 The specific haplotypes and the phenotype “MTX-intolerance”

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 0.348 0.402 −0.916 0.360 0.329
1 rs1801131-rs1801133 A-T 0.340 0.228 1.852 0.064 0.06
1 rs1801131-rs1801133 C-C 0.312 0.370 −0.914 0.361 0.324
1 rs1801131-rs1801133 C-T 0.000 0.000 NA NA NA
7 rs1045642-rs2032582 C-A 0.021 0.022 −0.048 0.962 1
7 rs1045642-rs2032582 C-G 0.401 0.435 −0.530 0.596 0.557
7 rs1045642-rs2032582 C-T 0.008 0.000 NA NA NA
7 rs1045642-rs2032582 T-G 0.154 0.174 −0.432 0.666 0.694
7 rs1045642-rs2032582 T-T 0.415 0.370 0.758 0.448 0.422
10 rs717620-rs2273697-rs3740066 A-A-A 0.000 0.000 NA NA NA
10 rs717620-rs2273697-rs3740066 A-G-A 0.201 0.250 −0.852 0.394 0.427
10 rs717620-rs2273697-rs3740066 A-G-G 0.000 NA NA NA NA
10 rs717620-rs2273697-rs3740066 G-A-A 0.023 0.018 NA NA NA
10 rs717620-rs2273697-rs3740066 G-A-G 0.227 0.221 0.070 0.944 0.961
10 rs717620-rs2273697-rs3740066 G-G-A 0.182 0.112 1.465 0.143 0.153
10 rs717620-rs2273697-rs3740066 G-G-G 0.367 0.399 −0.466 0.641 0.639
10 rs717620-rs2273697 A-A 0.000 0.000 NA NA NA
10 rs717620-rs2273697 A-G 0.201 0.250 −0.852 0.394 0.36
10 rs717620-rs2273697 G-A 0.250 0.239 0.168 0.867 0.84
10 rs717620-rs2273697 G-G 0.549 0.511 0.537 0.591 0.572
10 rs2273697-rs3740066 A-A 0.021 0.017 NA NA NA
10 rs2273697-rs3740066 A-G 0.229 0.223 0.110 0.913 0.936
10 rs2273697-rs3740066 G-A 0.386 0.364 0.376 0.707 0.732
10 rs2273697-rs3740066 G-G 0.364 0.397 −0.526 0.599 0.587
11 rs1176744-rs1062613-rs1985242-rs1176713 G-C-A-C 0.071 0.043 0.558 0.577 0.569
11 rs1176744-rs1062613-rs1985242-rs1176713 G-C-T-T 0.029 0.008 NA NA NA
11 rs1176744-rs1062613-rs1985242-rs1176713 G-T-A-T 0.220 0.156 1.153 0.249 0.265
11 rs1176744-rs1062613-rs1985242-rs1176713 T-C-A-C 0.041 0.035 0.066 0.948 0.972
11 rs1176744-rs1062613-rs1985242-rs1176713 T-C-T-T 0.000 0.051 NA NA NA
11 rs1176744-rs1062613-rs1985242-rs1176713 T-T-A-C 0.001 NA NA NA NA
11 rs1176744-rs1062613-rs1985242-rs1176713 T-T-A-T 0.029 0.063 −1.030 0.303 0.287
11 rs1176744-rs1062613-rs1985242 G-C-A NA 0.016 NA NA NA
11 rs1176744-rs1062613-rs1985242 G-C-T 0.513 0.496 0.406 0.685 0.693
11 rs1176744-rs1062613-rs1985242 G-T-A 0.048 0.098 −1.430 0.153 0.153
11 rs1176744-rs1062613-rs1985242 T-C-A 0.034 0.034 −1.283 0.199 0.142
11 rs1176744-rs1062613-rs1985242 T-C-T 0.016 NA NA NA NA
11 rs1176744-rs1062613-rs1985242 T-T-A 0.097 0.054 0.822 0.411 0.397
11 rs1176744-rs1062613-rs1985242 T-T-T 0.218 0.164 1.219 0.223 0.23
11 rs1062613-rs1985242-rs1176713 C-A-C 0.045 0.075 −1.052 0.293 0.276
11 rs1062613-rs1985242-rs1176713 C-A-T 0.001 NA NA NA NA
11 rs1062613-rs1985242-rs1176713 C-T-T 0.030 0.077 −1.331 0.183 0.186
11 rs1062613-rs1985242-rs1176713 T-A-C 0.516 0.488 0.355 0.722 0.735
11 rs1062613-rs1985242-rs1176713 T-A-T 0.078 0.142 −1.947 0.052 0.054
11 rs1062613-rs1985242-rs1176713 T-T-T 0.015 NA NA NA NA
11 rs1176744-rs1062613 G-C 0.099 0.106 −0.190 0.849 0.862
11 rs1176744-rs1062613 G-T 0.028 0.025 0.094 0.925 0.982
11 rs1176744-rs1062613 T-C 0.734 0.652 1.486 0.137 0.129
11 rs1176744-rs1062613 T-T 0.088 0.133 −1.048 0.295 0.302
11 rs1062613-rs1985242 C-A 0.034 0.084 −1.688 0.091 0.126
11 rs1062613-rs1985242 C-T 0.016 0.000 NA NA NA
11 rs1062613-rs1985242 T-A 0.323 0.224 1.489 0.137 0.137
11 rs1062613-rs1985242 T-T 0.038 0.070 −0.848 0.396 0.379
11 rs1985242-rs1176713 A-C 0.538 0.559 −0.078 0.937 0.953
11 rs1985242-rs1176713 A-T 0.101 0.148 −1.663 0.096 0.098
11 rs1985242-rs1176713 T-C 0.128 0.130 −0.136 0.892 0.868
11 rs1985242-rs1176713 T-T 0.734 0.652 1.488 0.137 0.126
12 rs2117032-rs4149056-rs4149081 C-C-A 0.082 0.045 0.914 0.361 0.392
12 rs2117032-rs4149056-rs4149081 C-C-G 0.000 0.000 NA NA NA
12 rs2117032-rs4149056-rs4149081 C-T-G 0.279 0.325 −0.596 0.551 0.554
12 rs2117032-rs4149056-rs4149081 C-T-T 0.092 0.097 0.172 0.864 0.855
12 rs2117032-rs4149056-rs4149081 T-C-A 0.014 0.022 NA NA NA
12 rs2117032-rs4149056-rs4149081 T-C-C 0.533 0.512 0.162 0.872 0.895
12 rs2117032-rs4149056-rs4149081 T-T-G 0.082 0.046 0.904 0.366 0.368
12 rs2117032-rs4149056 C-C 0.279 0.324 −0.593 0.553 0.566
12 rs2117032-rs4149056 C-T 0.091 0.096 0.177 0.860 0.828
12 rs2117032-rs4149056 T-C 0.547 0.535 0.039 0.969 0.984
12 rs2117032-rs4149056 T-T 0.174 0.141 0.660 0.509 0.586
12 rs4149056-rs4149081 C-A 0.014 0.022 NA NA NA
12 rs4149056-rs4149081 C-C 0.813 0.837 −0.490 0.624 0.681
12 rs4149056-rs4149081 C-G 0.082 0.045 0.914 0.361 0.392
12 rs4149056-rs4149081 C-T 0.000 0.000 NA NA NA
12 rs4149056-rs4149081 T-C 0.279 0.325 −0.596 0.551 0.554
12 rs4149056-rs4149081 T-G 0.092 0.097 0.172 0.864 0.855
12 rs4149056-rs4149081 T-T 0.014 0.022 NA NA NA
  1. The haplotype-specific scores for the listed markers in association with the parent-assessed MTX-induced nausea – the methotrexate intolerance severity score
  2. N = 118, due to missing SNP data for two patients and MISS data for one
  3. Chr Chromosome. Markers; the SNPs in the haplotype. Haplotypes; the alleles for the SNPs in the haplotype. Cases; MTXintolerant (n = 72). Controls; MTXtolerant (n = 46). 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)