Association of IFNGR2 Gene Polymorphisms with Pulmonary Tuberculosis Among the Vietnamese
Association of IFNGR2 gene polymorphisms with pulmonary tuberculosis among the Vietnamese
Human Genetics
Minako Hijikata, Junko Shojima, Ikumi Matsushita, Katsushi Tokunaga, Jun Ohashi, Nguyen T L Hang, Toru Horie, Shinsaku Sakurada, Nguyen P Hoang, Pham H Thuong, Luu T Lien, Naoto Keicho
Corresponding author: Naoto Keicho
Department of Respiratory Diseases, Research Institute, National Center for Global Health and Medicine, Tokyo 162-8655, Japan. E-mail:
Supplementary table 1 Allele frequencies of IFNGR2 microsatellite markers in 98 patients and 200 controls
Tuberculosis (n=98) / Controls(n=200)
Allele / Allele / 2x2
Alleles / No. / frequency / No. / frequency / P value
IFNGR2-MS1 / 325 / (TAAA)7 / 26 / 0.133 / 100 / 0.250 / 0.0009
337 / (TAAA)10 / 21 / 0.107 / 34 / 0.085 / 0.3710
341 / (TAAA)11 / 76 / 0.388 / 128 / 0.320 / 0.1182
345 / (TAAA)12 / 57 / 0.291 / 112 / 0.280 / 0.8467
others / 16 / 0.081 / 26 / 0.065 / 0.4966
IFNGR2-MS2 / 248 / (TG)9 / 113 / 0.577 / 215 / 0.538 / 0.3819
250 / (TG)10 / 54 / 0.276 / 86 / 0.215 / 0.1227
252 / (TG)11 / 20 / 0.102 / 81 / 0.203 / 0.0024
others / 9 / 0.046 / 18 / 0.045 / 1.0000
Association of IFNGR2 gene polymorphisms with pulmonary tuberculosis among the Vietnamese. Human Genetics. Hijikata et al.
Supplementary table 2 Association results for selected SNPs in 273 patients (panel A) and 506 controls
SNP / HapMap position / Alleles / Controls / Patients / Allele / HWE P-value
(Chromosome 21) / (Major:minor) / MAF / MAF / P value / (control) / LD blocks
1 / rs999259 / 33588362 / C:T / IL10RB / 0.393 / 0.396 / 0.9092 / 0.1861 / 1
2 / rs1058867 / 33591251 / A:G / IL10RB / 0.199 / 0.175 / 0.2504 / 0.4591
3 / rs1012334 / 33635621 / A:T / IFNAR1 / 0.461 / 0.476 / 0.5809 / 0.3831 / 2
4 / rs2257167 / 33637569 / G:C / IFNAR1 / 0.426 / 0.448 / 0.4004 / 0.0037
5 / rs2243600 / 33645531 / G:T / IFNAR1 / 0.384 / 0.382 / 0.9428 / 0.1473 / 3
6 / rs1041868 / 33649200 / G:A / IFNAR1 / 0.419 / 0.448 / 0.2695 / 0.0163
7 / rs9974246 / 33667726 / G:A / 0.490 / 0.492 / 0.9302 / 0.1490 / 4
8 / rs2834208 / 33674633 / A:C / 0.464 / 0.456 / 0.7557 / 0.5931
9 / rs11702844 / 33681746 / A:G / 0.366 / 0.375 / 0.7020 / 1.0000
10 / rs11088251 / 33692680 / A:C / 0.349 / 0.366 / 0.5040 / 0.8352 / 5
IFNGR2-MS1* / 33695817 / others:325 / IFNGR2 / 5' near gene / 0.250 / 0.133 / 0.0010 / 0.2762
11 / rs8134145 / 33697304 / A:C / IFNGR2 / promoter / 0.378 / 0.405 / 0.3093 / 0.6842
12 / rs8126756 / 33697314 / T:C / IFNGR2 / promoter / 0.377 / 0.403 / 0.3248 / 0.7722
13 / rs17882748 / 33697591 / C:T / IFNGR2 / promoter / 0.385 / 0.403 / 0.4982 / 0.7813
14 / rs2284553 / 33698565 / G:A / IFNGR2 / intron1 / 0.370 / 0.407 / 0.1570 / 0.9063
15 / rs2268241 / 33702920 / G:A / IFNGR2 / intron1 / 0.383 / 0.412 / 0.2773 / 0.6989
16 / rs2300372 / 33706325 / C:T / IFNGR2 / intron1 / 0.093 / 0.106 / 0.4296 / 1.0000
17 / rs9808753 / 33709182 / A:G / IFNGR2 / exon2 / 0.383 / 0.408 / 0.3415 / 0.8145
18 / rs2834211 / 33711678 / T:C / IFNGR2 / intron2 / 0.234 / 0.254 / 0.3784 / 1.0000
IFNGR2-MS2* / 33713638 / others:252 / IFNGR2 / intron2 / 0.202 / 0.102 / 0.0073 / 0.0326
19 / rs2834213 / 33714780 / A:G / IFNGR2 / intron2 / 0.220 / 0.163 / 0.0088 / 0.2830
20 / rs1059293 / 33731563 / T:C / IFNGR2 / exon7 (3'UTR) / 0.233 / 0.176 / 0.0030 / 0.1973
21 / rs2834226 / 33749710 / C:A / TMEM50B / 0.247 / 0.272 / 0.2694 / 0.8456
22 / rs743335 / 33762388 / T:A / TMEM50B / 0.132 / 0.144 / 0.5254 / 0.7172
23 / rs4817574 / 33767271 / G:C / TMEM50B / 0.430 / 0.440 / 0.7042 / 0.3065 / 6
24 / rs2850030 / 33776581 / T:C / TMEM50B / 0.439 / 0.421 / 0.5007 / 0.9616
25 / rs4817575 / 33782055 / G:A / 0.225 / 0.264 / 0.0887 / 0.1219 / 7
26 / rs3761347 / 33786154 / T:C / DNAJC28 / 0.225 / 0.267 / 0.0679 / 0.1291
27 / rs7283354 / 33798940 / C:T / GART / 0.236 / 0.282 / 0.0458 / 0.2764
28 / rs4817580 / 33836467 / G:A / GART / 0.227 / 0.272 / 0.0515 / 0.2140
29 / rs7279549 / 33838483 / C:T / SON / 0.241 / 0.284 / 0.0618 / 0.8844
30 / rs9978525 / 33869726 / A:C / SON / 0.419 / 0.416 / 0.9063 / 0.1632
31 / rs3761352 / 33934999 / T:C / CRYZL1 / 0.308 / 0.263 / 0.0602 / 1.0000
32 / rs1892700 / 33938007 / G:A / CRYZL1 / 0.199 / 0.156 / 0.0369 / 0.1997
MAF: minor allele frequency; HWE: Hardy-Weinberg equilibrium; LD: linkage disequilibrium; UTR: untranslated region
*microsatellite markers were analyzed in 98 patients and 200 controls.
Association of IFNGR2 gene polymorphisms with pulmonary tuberculosis among the Vietnamese.
Human Genetics. Hijikata et al.
Supplementary table 3 Estimated haplotype frequencies of the SNPs in the IFNGR2 region
Frequency / PermutationHaplotype / Controls / Tuberculosis / P value
H1 / CCCGACGTAT / 0.375 / 0.397 / NS
H2 / ATCGGCATGC / 0.217 / 0.164 / 0.034
H3 / ATTAGCACAT / 0.140 / 0.148 / NS
H4 / ATTAGCATAT / 0.127 / 0.132 / NS
H5 / ATTAGTACAT / 0.086 / 0.095 / NS
Haplotypes (H) 1-5 with frequencies > 0.02 were estimated in 273 patients and in 506 controls using 10 SNPs (rs8134145, rs8126756, rs17882748, rs2284553, rs2268241, rs2300372, rs9808753, rs2834211, rs2834213, rs1059293) of IFNGR2. P values by permutation test with 100,000 replications by Haploview are shown. Bold-underlined letters indicates promoter haplotype ATC, intron 2 G and 3’ UTR C. NS: not significant
Association of IFNGR2 gene polymorphisms with pulmonary tuberculosis among the Vietnamese. Human Genetics. Hijikata et al.
Supplementary figure 1 Pairwise linkage disequilibrium (LD) between associated alleles of microsatellite markers and 32 SNPs
Figure legend
(Upper panel) Pairwise LD (D’ and r2) between associated alleles of microsatellite markers and 32 SNPs are shown. In the calculation of pairwise LD, microsatellite alleles except for one showing the smallest P value were grouped, and the microsatellite locus was regarded as having only two alleles. Both IFNGR2-MS1-325 allele and IFNGR2- MS2-252 allele were in strong LD with rs2834213 and rs1059293, and were in the same LD block.
(Lower panel) Pairwise LD (D’) between 32 SNPs and 2 microsatellite markers determined by the Haploview program are shown.