Table 5.

Distribution of Haplotype Frequencies for Controls and Crohn’s Disease Subjects in Discovery and Combined Cohorts

Haplotype	Frequency Controls	Frequency CD	P Value
Discovery Cohort
Block 1
GCCCGCTC	0.616	0.585	0.193
CGTCACTC	0.143	0.195	0.004*
GCCGGTCA	0.145	0.134	0.532
GCCCGTCA	0.075	0.062	0.265
Block 2
AG	0.373	0.356	0.469
CG	0.314	0.343	0.193
AC	0.313	0.300	0.572
Block 3
TTG	0.522	0.531	0.727
CGA	0.257	0.249	0.700
TGA	0.204	0.211	0.732
Block 4
GT	0.606	0.603	0.897
GC	0.300	0.299	0.972
AC	0.091	0.097	0.681
Block 5
CC	0.471	0.457	0.568
CT	0.304	0.306	0.909
TT	0.224	0.233	0.645
Block 6
GGC	0.405	0.394	0.640
GGT	0.362	0.366	0.859
AAT	0.224	0.230	0.760
Replication Cohort
Block 1
GCCCGCTC	0.593	0.608	0.453
CGTCACTC	0.130	0.171	0.004*
GCCGGTCA	0.140	0.143	0.869
GCCCGTCA	0.089	0.071	0.128
Combined Cohorts
Block 1
GCCCGCTC	0.600	0.595	0.755
CGTCACTC	0.136	0.185	7.755 × 10−6**
GCCGGTCA	0.142	0.139	0.775
GCCCGTCA	0.083	0.067	0.045*

Haplotype analyses were performed on the SNPs within each block of high linkage disequilibrium. Haplotype analysis was carried out using HAPLOVIEW Software, version 3.11, with haplotype blocks created using the confidence interval feature. The association of specific haplotypes within blocks with the outcome was examined and P values were estimated. CD= Crohn’s disease.

^*P<0.05;

^**P<2.09 × 10⁻⁴ after correcting for 27 haplotype comparisons.