When logistic regression was used to carry out association analysis after modelling the SNP effects as additive, dominant or recessive, SNP6 (rs7749390, located on the splice site of the exon/intron of ifngr1 gene) showed a significant difference in co-dominant (OR: 1.86, 95% CI: 1.04–3.31) and log-additive (OR: 1.35, Galunisertib cell line 95% CI: 1.02–1.80) models, and P-values were <0.05 after adjustment for sex (Table 4). The log-additive model was accepted as the best inheritance model because of the smaller Akaike information criterion (AIC) value

(565.6). The other SNP showed no association with tuberculosis in any of the five inheritance models (all P > 0.05, data not shown). Pairwise LD between the three SNP of the ifng gene and the other four SNP of ifngr1 was calculated for the cases and controls in the Chinese Han population. The three SNP of the ifng gene had no association with tuberculosis (data not shown). D′ and r for all possible pairs of the SNP in the ifngr1 gene are shown in Table 5. We found strong LD (D′ > 0.75) between the following pairs of the markers in the ifngr1 gene: SNP4/SNP5 (D′ = 0.941), SNP4/SNP6 (D′ = 0.830) and SNP5/SNP6 HER2 inhibitor (D′ = 0.998). Therefore, we constructed SNP4/SNP5/SNP6/SNP7 as haplotype blocks in the ifngr1 gene (because the distance was about 141 bp between SNP6 and

SNP7, SNP7 was list to the haplotype analysis). The frequencies of the estimated haplotypes are presented in Table 6. The association analysis of the haplotypes with tuberculosis is shown in Table 6. The haplotype of SNP4/SNP5/SNP6/SNP7 showed significant association with the disease (P = 0.00079). The HSP90 C-A-A-TT haplotype was observed more frequently in the cases than in the controls (OR: 3.96, 95% CI: 1.90–8.21). The association analysis of haplotypes was adjusted also by sex. In China, tuberculosis is still prevalent with about 5 million cases every year. As only about 10% of the population that

is infected by M. tuberculosis will develop clinical tuberculosis, differences in host immunity and genetic factors may account for the development of tuberculosis after infection [3]. In this study, we tested the hypothesis that the ifng and ifngr1 genes play a role in the pathogenesis of tuberculosis. Seven SNP in these two genes were selected as the gene markers for association analysis. It is accepted generally that IFN-γ plays a pivotal role in the pathogenesis of tuberculosis [7]. Abnormality of the ifng gene is considered as one of the causative factors [8]. An initial study of the association of the ifng gene with tuberculosis indicated that allele A of the +874 A/T in the first intron region was a susceptibility factor for M. tuberculosis infection, both by population- and family-based analysis.