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Table 4 Haplotype analysis of IBD patients and non-IBD controls

From: Association of genetic variation in the NR1H4 gene, encoding the nuclear bile acid receptor FXR, with inflammatory bowel disease

Order Haplotype a) b) c) d) e) Cases (%) Controls (%) OR (C.I.) P Order Haplotype a) b) c) d) e) Cases (%) Controls (%) OR (C.I.) P
1 G G A G G 405.9 (52.2) 510.1 (52.6) 0.98 (0.81-1.19)   1 G G A G G 417 (53.6) 530 (54.6) 0.96 (0.79-1.16) a) ns
2 G G A G C 243.9 (31.3) 261 (26.9) 1.24 (1.01-1.53) 0.064 2 G G A G C 235 (30.2) 241 (24.7) 1.31 (1.06-1.62) a) 0.012
3 G G A A C 55.9 (7.2) 91.3 (9.4) 0.75 (0.53-1.05) 0.091 3 G G A A C 63 (8.1) 108 (11.1) 0.7 (0.51-0.97) a) 0.03
4 G G A A G 27.4 (3.5) 47.5 (4.9) 0.71 (0.44-1.14)   4 G G A A G 18 (2.3) 31 (3.2) 0.72 (0.40-1.29) a) ns
5 A G A G G 2.7 (0.4) 13.4 (1.4) 0.25 (0.07-0.93) 0.017 5 A G A G G 2 (0.3) 13 (1.3) 0.19 (0.04-0.84) 0.017
6 A G A G C 6.6 (0.8) 12 (1.2) 0.68 (0.26-1.76)   6 A G A G C 8 (1.0) 14 (1.4) 0.71 (0.30-1.70) ns
7 G G T G C 5 (0.6) 9.1 (0.9) 0.68 (0.23-2.04)   7 G G T G C 4 (0.5) 9 (0.9) 0.55 (0.17-1.80) ns
8 G T A G G 3.8 (0.5) 7.5 (0.8) 0.63 (0.18-2.17) NA 8 G T A G G 2 (0.3) 7 (0.7) 0.35 (0.07-1.71) ns
9 G T A G C 10.4 (1.3) 5.7 (0.6) 2.27 (0.82-6.32) 0.090 9 G T A G C 12 (1.5) 6 (0.6) 2.52 (0.94-6.74) ns
10 G G T G G 2 (0.3) 3.1 (0.3) 0.79 (0.13-4.70) NA 10 G G T G G 1 (0.1) 2 (0.2) 0.62 (0.06-6.89) ns
11 G T A A G 0.8 (0.1) 1.8 (0.2) NA NA 11 G T A A G 1 (0.1) 2 (0.2) 0.63 (0.06-6.89) ns
12 A G A A G 0.2 (0) 2.0 (0.2) 0.13 (0–11.93) NA 12 A G A A G 0 1 (0.1) NA ns
13 G G T A C 2.4 (0.3) 2.3 (0.2) 1.29 (0.21-7.99) NA 13 G G T A C 4 (0.5) 4 (0.4) 1.25 (0.31-5.00) ns
14 G T T G C 7.4 (1) 1.0 (0.1) NA NA 14 G T T G C 7 (0.9) 1 (0.1) 8.80 (1.08-71.70) 0.026
15 G G T A G 1.1 (0.1) 0.5 (0.1) NA NA 15 G G T A G 1 (0.1) 0 NA ns
16 G T T A G 1.2 (0.2) 1.0 (0.1) NA NA 16 G T T A G 3 (0.4) 1 (0.1) 3.75 (0.39-36.15) ns
17 A G A A C 0.1 (0) 0.6 (0.1) NA NA 17 A G A A C 0 0 NA NA
18 A T A G C 0.4 (0.1) 0 (0) NA NA 18 A T A G C 0 0 NA NA
19 G T T A C 1 (0.1) 0 (0) NA NA 19 G T T A C 0 0 NA NA
  1. 389 cases (778 haplotypes) and 485 controls (970 haplotypes) were included in the analysis.
  2. Global haplotype distribution: P = 0.003.
  3. Left table side: Predicted haplotypes obtained with Monte Carlo simulations using FAMHAP. The calculation of odds ratios and a global P value for haplotype distribution was performed on these results using FAMHAP. The haplotype order follows a priority ranking within the control group. Nineteen haplotypes were predicted. The haplotype base positions correspond to a) rs3863377, b) rs56163822, c) rs7138843, d) rs10860603, and e) rs35724. As FAMHAP tested all haplotypes with a frequency >0.01, the frequency distribution of eight haplotypes (1–7, 9) was included. Relevant P-values for four haplotypes were displayed by FAMHAP. None of the individual haplotypes are significantly differentially distributed between the IBD and control groups.
  4. OR, odds ratio; NA, not applicable, FAMHAP did not calculate an odds ratio on these results because of a low haplotype frequency value predicted.
  5. Right table side (italics): Most likely occurring haplotype frequencies (haplotype in best reconstruction) predicted by FAMHAP. Based on these predictions significance tests were performed. P-values were calculated using the Fisher’s exact test or (if marked with a) ) using the Chi-Square test. A Bonferroni-corrected P-value of 0.003 (19 tests) was taken as significance level. According to this, none of the haplotypes appeard to be significantly differently distributed between the case and control groups.
  6. OR, odds ratio; C.I., confidence interval; NA, OR not applicable because of at least one cell count with the value of null; ns, not significant and P >0.05.