Supplementary Table 1. SNPs in the SP110 region.

# / dbSNP / Alleles / Location / SNP origin / Position in NCBI35 / MAFa / Allelic r2 for
non-genotyped SNPs
1 / rs1465530 / G>A / SP140 intron / HapMap / 230,934,433 / 0.372 / genotyped
2 / rs2288328 / G>C / SP140 intron / HapMap / 230,931,749 / 0.298 / 0.95
3 / rs2278197 / C>T / SP140 intron / HapMap / 230,928,690 / 0.372 / 1.00
4 / rs11687292 / G>A / SP140 intron / HapMap / 230,924,709 / 0.160 / 0.91
5 / rs6709625 / G>A / SP140 intron / HapMap / 230,924,675 / 0.277 / 0.90
6 / rs6436922 / T>C / SP140 intron / HapMap / 230,923,545 / 0.191 / genotyped
7 / rs1946409 / G>C / SP140 intron / HapMap / 230,918,673 / 0.096 / genotyped
8 / rs13397985 / A>C / SP140 intron / HapMap / 230,916,728 / 0.181 / 0.88
9 / rs11695193 / T>A / intergenic / HapMap / 230,915,520 / 0.149 / 0.95
10 / rs10209615 / A>G / intergenic / HapMap / 230,915,448 / 0.160 / 0.92
11 / rs11679983 / C>T / SP110 intron / HapMap / 230,909,806 / 0.160 / genotyped
12 / ss65624498 / G>A / SP110 intron / sequencing, novel / 230,908,813 / 0.029 / MAF < 0.05
13 / ss65624499 / G>A / SP110 intron / sequencing, novel / 230,908,684 / 0.021 / MAF < 0.05
14 / rs6738805 / A>G / SP110 intron / HapMap, sequencing / 230,908,676 / 0.159 / genotyped
15 / ss65624501 / T>C / SP110 intron / sequencing, novel / 230,908,637 / 0.448 / 0.80
16 / rs7573954 / G>A / SP110 intron / sequencing / 230,908,616 / 0.260 / genotyped
17 / rs1346311 / C>T / SP110 intron / sequencing / 230,907,892 / 0.171 / genotyped
18 / rs13389060 / C>A / SP110 intron / sequencing / 230,907,629 / 0.252 / genotyped
19 / rs1966555 / G>A / SP110 intron / sequencing / 230,907,439 / 0.468 / genotyped
20 / ss65624506 / C>T / SP110 intron / sequencing, novel / 230,907,390 / 0.108 / 0.69
21 / ss65624507 / G>A / SP110 intron / sequencing, novel / 230,907,389 / 0.021 / MAF < 0.05
22 / ss65624508 / T>C / SP110 exon 2 / sequencing, novel / 230,907,073 / 0.000 / MAF < 0.05
23 / rs7580912 / A>G / SP110 intron / sequencing / 230,906,910 / 0.288 / genotyped
24 / rs7580900 / A>G / SP110 intron / HapMap, sequencing / 230,906,889 / 0.447 / 0.82
25 / ss65624511 / T>C / SP110 intron / sequencing, novel / 230,905,364 / 0.011 / MAF < 0.05
26 / ss65624512 / C>G / SP110 intron / sequencing, novel / 230,905,103 / 0.000 / MAF < 0.05
27 / rs3177554 / C>T / SP110 exon 4 (W112R) / HapMap, sequencing / 230,903,230 / 0.158 / genotyped
28 / ss65624514 / G>A / SP110 exon 4 (G126S) / sequencing, novel / 230,903,188 / 0.000 / genotyped
29 / rs11556887 / C>T / SP110 exon 4 (A128V) / sequencing / 230,903,181 / 0.000 / genotyped
30 / ss65624516 / C>A / SP110 exon 4 / sequencing, novel / 230,903,003 / 0.036 / MAF < 0.05
31 / ss65624517 / C>A / SP110 intron / sequencing, novel / 230,902,947 / 0.033 / MAF < 0.05
32 / ss65624518 / G>A / SP110 intron / sequencing, novel / 230,902,773 / 0.053 / genotyped
33 / ss65624519 / C>T / SP110 intron / sequencing, novel / 230,902,659 / 0.223 / 0.71
34 / ss65624520 / C>T / SP110 exon 5 (A206V) / sequencing, novel / 230,902,617 / 0.265 / 0.65
35 / rs11556888 / G>A / SP110 exon 5 (E207K) / sequencing / 230,902,615 / 0.117 / 0.63
36 / rs3820974 / A>C / SP110 intron / HapMap, sequencing / 230,901,794 / 0.426 / 0.80
37 / ss65624523 / C>A / SP110 intron / sequencing, novel / 230,901,622 / 0.000 / MAF < 0.05
38 / ss65624524 / C>T / SP110 intron / sequencing, novel / 230,901,566 / 0.016 / MAF < 0.05
39 / rs3769837 / A>C / SP110 intron / sequencing / 230,901,537 / 0.239 / 0.83
40 / rs2114592 / C>T / SP110 intron / HapMap / 230,900,711 / 0.106 / 0.99
41 / ss65624526 / C>G / SP110 intron / sequencing, novel / 230,900,263 / 0.011 / MAF < 0.05
42 / rs1365776 / A>G / SP110 exon 8 (G299R) / sequencing / 230,898,214 / 0.412 / genotyped
43 / ss65624528 / C>G / SP110 intron / sequencing, novel / 230,898,179 / 0.017 / MAF < 0.05
44 / ss65624529 / A>G / SP110 intron / sequencing, novel / 230,898,074 / 0.081 / genotyped
45 / ss65624530 / T>A / SP110 intron / sequencing, novel / 230,891,227 / 0.107 / genotyped
46 / rs1124534 / G>A / SP110 intron / HapMap / 230,889,974 / 0.106 / 0.99
47 / rs930032 / A>T / SP110 intron / HapMap / 230,884,953 / 0.245 / 0.94
48 / rs1896258 / A>G / SP110 intron / HapMap / 230,884,459 / 0.245 / 0.94
49 / rs6735604 / T>C / SP110 intron / HapMap / 230,881,320 / 0.245 / 0.94
50 / rs3948464 / C>T / SP110 exon 11 (L425S) / HapMap, sequencing / 230,876,220 / 0.156 / genotyped
51 / rs2114591 / C>T / SP110 intron / HapMap / 230,876,074 / 0.426 / 0.92
52 / rs958978 / T>C / SP110 intron / HapMap / 230,875,491 / 0.245 / 0.94
53 / rs4973287 / A>G / SP110 intron / sequencing / 230,873,447 / 0.229 / genotyped
54 / rs4973286 / A>G / SP110 intron / sequencing / 230,873,435 / 0.238 / genotyped
55 / rs919178 / A>G / SP110 intron / HapMap / 230,869,969 / 0.394 / 0.84
56 / rs2241525 / G>A / SP110 intron / sequencing / 230,868,307 / 0.128 / genotyped
57 / rs1804027 / T>C / SP110 exon 14 (M523T) / HapMap, sequencing / 230,867,781 / 0.489 / genotyped
58 / ss65624536 / T>C / SP110 alternative exon / sequencing, novel / 230,866,780 / 0.000 / MAF < 0.05
59 / ss65624537 / T>C / SP110 intron / sequencing, novel / 230,866,611 / 0.109 / 0.80
60 / rs1004869 / G>T / SP110 intron / HapMap / 230,864,776 / 0.096 / 0.85
61 / rs1004868 / C>T / SP110 intron / HapMap / 230,864,415 / 0.096 / 0.85
62 / rs10498244 / A>G / SP110 intron / HapMap / 230,863,338 / 0.298 / 0.92
63 / ss65624538 / T>C / SP110 exon 15 / sequencing, novel / 230,863,121 / 0.096 / 1.00
64 / rs13018234 / C>T / SP110 exon 16 / sequencing / 230,862,371 / 0.096 / 0.85
65 / rs3948463 / G>A / SP110 exon 16 (M579I) / sequencing / 230,862,365 / 0.096 / genotyped
66 / ss65624541 / T>C / SP110 intron / sequencing, novel / 230,862,259 / 0.105 / 0.78
67 / rs12988385 / A>G / SP110 intron / sequencing / 230,861,816 / 0.141 / genotyped
68 / rs11690519 / G>A / SP110 intron / sequencing / 230,861,802 / 0.066 / genotyped
69 / ss65624544 / C>T / SP110 intron / sequencing, novel / 230,861,032 / 0.020 / MAF < 0.05
70 / ss65624545 / C>T / SP110 intron / sequencing, novel / 230,861,019 / 0.007 / MAF < 0.05
71 / ss65624546 / T>A / SP110 intron / sequencing, novel / 230,860,806 / 0.028 / MAF < 0.05
72 / rs6436915 / C>A / SP110 intron / HapMap / 230,860,029 / 0.426 / 0.93
73 / ss65624547 / G>A / intergenic / sequencing, novel / 230,859,074 / 0.047 / MAF < 0.05
74 / rs722555 / A>G / intergenic / sequencing / 230,859,021 / 0.453 / genotyped
75 / rs7583955 / G>T / intergenic / sequencing / 230,858,793 / 0.362 / genotyped
76 / ss65624550 / T>C / intergenic / sequencing, novel / 230,858,765 / 0.021 / MAF < 0.05
77 / rs6726359 / A>T / intergenic / HapMap / 230,854,943 / 0.277 / 0.83
78 / rs890580 / C>T / intergenic / HapMap / 230,852,667 / 0.223 / genotyped
79 / rs1427286 / T>A / intergenic / HapMap / 230,852,099 / 0.117 / 0.88
80 / rs6436913 / C>G / intergenic / HapMap / 230,849,292 / 0.149 / 0.89
81 / rs4973277 / C>T / intergenic / HapMap / 230,845,758 / 0.149 / 0.89
82 / rs4973275 / A>G / intergenic / HapMap / 230,840,010 / 0.181 / genotyped
83 / rs1365773 / T>G / intergenic / HapMap / 230,835,059 / 0.181 / 1.00

a MAF, minor allele frequency in the 48 CEU individuals. When MAF = 0 the SNP has been identified among 48 Russian subjects.

Supplementary Table 2. Allele and genotype frequencies of the 29 genotyped SNPs in the SP110 gene separately in the samples from St. Petersburg and Samara.

SNP

/ Allele / Region / TB / Controls
1/2 / 11 / % / 12 / % / 22 / % / 11 / % / 12 / % / 22 / %
rs1465530 / G/A / St Petersburg / 696 / (46.3) / 632 / (42.0) / 175 / (11.6) / 720 / (45.5) / 695 / (43.9) / 169 / (10.7)
Samara / 169 / (44.9) / 170 / (45.2) / 37 / (9.8) / 239 / (49.2) / 207 / (42.6) / 40 / (8.2)
rs6436922 / G/A / St Petersburg / 34 / (2.3) / 448 / (30.6) / 982 / (67.1) / 64 / (4.1) / 480 / (30.9) / 1,010 / (65.0)
Samara / 10 / (2.7) / 121 / (32.3) / 244 / (65.1) / 16 / (3.3) / 160 / (33.1) / 308 / (63.6)
rs1946409 / C/G / St Petersburg / 4 / (0.3) / 186 / (12.2) / 1,329 / (87.5) / 5 / (0.3) / 184 / (11.6) / 1,401 / (88.1)
Samara / 1 / (0.3) / 47 / (12.5) / 329 / (87.3) / 0 / (0.0) / 63 / (13.2) / 415 / (86.8)
rs11679983 / C/T / St Petersburg / 1,075 / (71.9) / 379 / (25.3) / 42 / (2.8) / 1,093 / (69.5) / 444 / (28.2) / 36 / (2.3)
Samara / 275 / (72.8) / 93 / (24.6) / 10 / (2.6) / 359 / (75.1) / 110 / (23.0) / 9 / (1.9)
rs6738805 / C/T / St Petersburg / 27 / (1.8) / 382 / (25.8) / 1,074 / (72.4) / 45 / (2.9) / 416 / (26.6) / 1,101 / (70.5)
Samara / 8 / (2.2) / 100 / (27.1) / 261 / (70.7) / 11 / (2.3) / 147 / (30.5) / 324 / (67.2)
rs7573954 / G/A / St Petersburg / 563 / (40.2) / 650 / (46.4) / 188 / (13.4) / 587 / (39.8) / 693 / (47.0) / 196 / (13.3)
Samara / 145 / (39.2) / 184 / (49.7) / 41 / (11.1) / 193 / (40.6) / 224 / (47.2) / 58 / (12.2)
rs1346311 / A/G / St Petersburg / 27 / (1.8) / 361 / (23.9) / 1,121 / (74.3) / 26 / (1.6) / 321 / (20.2) / 1,239 / (78.1)
Samara / 6 / (1.6) / 98 / (25.6) / 279 / (72.8) / 15 / (3.0) / 125 / (25.3) / 355 / (71.7)
rs13389060 / C/A / St Petersburg / 1,116 / (74.3) / 358 / (23.8) / 28 / (1.9) / 1,241 / (78.3) / 317 / (20.0) / 26 / (1.6)
Samara / 276 / (72.8) / 97 / (25.6) / 6 / (1.6) / 350 / (72.2) / 121 / (24.9) / 14 / (2.9)
rs1966555 / G/A / St Petersburg / 353 / (24.3) / 738 / (50.7) / 364 / (25.0) / 404 / (26.2) / 784 / (50.9) / 352 / (22.9)
Samara / 84 / (23.0) / 203 / (55.5) / 79 / (21.6) / 100 / (21.2) / 255 / (54.0) / 117 / (24.8)
rs7580912 / C/T / St Petersburg / 212 / (14.3) / 686 / (46.3) / 583 / (39.4) / 222 / (14.3) / 710 / (45.8) / 617 / (39.8)
Samara / 42 / (11.3) / 184 / (49.5) / 146 / (39.2) / 64 / (13.2) / 234 / (48.1) / 188 / (38.7)
rs3177554 / A/G / St Petersburg / 16 / (1.1) / 232 / (15.6) / 1,235 / (83.3) / 12 / (0.8) / 258 / (16.7) / 1,275 / (82.5)
Samara / 4 / (1.1) / 58 / (15.3) / 317 / (83.6) / 3 / (0.6) / 78 / (16.0) / 406 / (83.4)
ss65624514 / G/A / St Petersburg / 1,469 / (97.3) / 40 / (2.7) / 0 / (0.0) / 1,554 / (97.4) / 40 / (2.5) / 1 / (0.1)
Samara / 369 / (96.6) / 13 / (3.4) / 0 / (0.0) / 475 / (96.2) / 19 / (3.8) / 0 / (0.0)
rs11556887 / T/C / St Petersburg / 36 / (2.4) / 323 / (21.4) / 1,150 / (76.2) / 29 / (1.8) / 372 / (23.4) / 1,191 / (74.8)
Samara / 7 / (1.8) / 74 / (19.4) / 300 / (78.7) / 14 / (2.9) / 118 / (24.2) / 356 / (73.0)
ss65624518 / G/A / St Petersburg / 1,439 / (95.0) / 75 / (5.0) / 0 / (0.0) / 1,496 / (94.3) / 90 / (5.7) / 1 / (0.1)
Samara / 345 / (91.8) / 29 / (7.7) / 2 / (0.5) / 463 / (94.3) / 28 / (5.7) / 0 / (0.0)
rs1365776 / G/A / St Petersburg / 261 / (17.2) / 704 / (46.3) / 554 / (36.5) / 262 / (16.6) / 771 / (48.7) / 549 / (34.7)
Samara / 68 / (17.8) / 173 / (45.2) / 142 / (37.1) / 71 / (14.5) / 235 / (47.9) / 185 / (37.7)
ss65624529 / G/A / St Petersburg / 5 / (0.3) / 160 / (10.6) / 1,338 / (89.0) / 7 / (0.4) / 145 / (9.1) / 1,439 / (90.4)
Samara / 4 / (1.1) / 30 / (7.9) / 345 / (91.0) / 1 / (0.2) / 45 / (9.1) / 447 / (90.7)
ss65624530 / T/A / St Petersburg / 1,127 / (76.0) / 319 / (21.5) / 36 / (2.4) / 1,158 / (74.0) / 377 / (24.1) / 30 / (1.9)
Samara / 303 / (80.2) / 66 / (17.5) / 9 / (2.4) / 353 / (72.5) / 120 / (24.6) / 14 / (2.9)
rs3948464 / A/G / St Petersburg / 20 / (1.3) / 262 / (17.4) / 1,227 / (81.3) / 15 / (1.0) / 292 / (18.5) / 1,270 / (80.5)
Samara / 4 / (1.0) / 61 / (16.0) / 316 / (82.9) / 3 / (0.6) / 79 / (16.0) / 411 / (83.4)
rs4973287 / G/A / St Petersburg / 85 / (5.6) / 514 / (34.1) / 909 / (60.3) / 91 / (5.7) / 565 / (35.6) / 929 / (58.6)
Samara / 18 / (4.7) / 117 / (30.7) / 246 / (64.6) / 28 / (5.7) / 180 / (36.4) / 287 / (58.0)
rs4973286 / G/A / St Petersburg / 85 / (5.8) / 493 / (33.8) / 881 / (60.4) / 86 / (5.6) / 549 / (35.8) / 898 / (58.6)
Samara / 18 / (4.8) / 119 / (31.8) / 237 / (63.4) / 27 / (5.6) / 172 / (35.8) / 281 / (58.5)
rs2241525 / C/T / St Petersburg / 1,115 / (74.7) / 353 / (23.7) / 24 / (1.6) / 1,212 / (77.1) / 334 / (21.3) / 25 / (1.6)
Samara / 291 / (76.2) / 82 / (21.5) / 9 / (2.4) / 371 / (76.3) / 109 / (22.4) / 6 / (1.2)
rs1804027 / A/G / St Petersburg / 433 / (29.2) / 731 / (49.3) / 320 / (21.6) / 445 / (28.1) / 773 / (48.9) / 364 / (23.0)
Samara / 132 / (35.4) / 170 / (45.6) / 71 / (19.0) / 155 / (32.3) / 231 / (48.1) / 94 / (19.6)
rs3948463 / C/T / St Petersburg / 1,277 / (84.9) / 216 / (14.4) / 12 / (0.8) / 1,352 / (85.5) / 218 / (13.8) / 12 / (0.8)
Samara / 338 / (88.7) / 40 / (10.5) / 3 / (0.8) / 412 / (85.3) / 69 / (14.3) / 2 / (0.4)
rs12988385 / G/A / St Petersburg / 20 / (1.3) / 222 / (14.8) / 1,254 / (83.8) / 14 / (0.9) / 264 / (16.6) / 1,312 / (82.5)
Samara / 1 / (0.3) / 64 / (17.0) / 312 / (82.8) / 3 / (0.6) / 77 / (15.8) / 407 / (83.6)
rs11690519 / C/T / St Petersburg / 1,372 / (94.2) / 84 / (5.8) / 0 / (0.0) / 1,465 / (94.6) / 83 / (5.4) / 1 / (0.1)
Samara / 353 / (92.9) / 27 / (7.1) / 0 / (0.0) / 471 / (96.3) / 18 / (3.7) / 0 / (0.0)
rs722555 / G/A / St Petersburg / 269 / (18.0) / 740 / (49.4) / 488 / (32.6) / 286 / (18.2) / 735 / (46.8) / 549 / (35.0)
Samara / 78 / (20.6) / 191 / (50.5) / 109 / (28.8) / 99 / (20.1) / 254 / (51.6) / 139 / (28.3)
rs7583955 / A/C / St Petersburg / 157 / (10.8) / 655 / (45.1) / 641 / (44.1) / 143 / (9.4) / 671 / (44.1) / 706 / (46.4)
Samara / 51 / (14.0) / 160 / (44.1) / 152 / (41.9) / 61 / (13.0) / 220 / (47.0) / 187 / (40.0)
rs890580 / A/G / St Petersburg / 77 / (5.1) / 542 / (36.0) / 886 / (58.9) / 101 / (6.4) / 570 / (36.0) / 914 / (57.7)
Samara / 20 / (5.2) / 133 / (34.8) / 229 / (59.9) / 29 / (6.0) / 185 / (38.1) / 272 / (56.0)
rs4973275 / A/G / St Petersburg / 934 / (62.2) / 495 / (33.0) / 73 / (4.9) / 953 / (60.5) / 550 / (34.9) / 71 / (4.5)
Samara / 233 / (63.0) / 127 / (34.3) / 10 / (2.7) / 276 / (57.6) / 183 / (38.2) / 20 / (4.2)

Titles and legends to figures

Supplementary Figure 1. SP110 gene region.

Three alternatively spliced transcripts of SP110 are shown. Resequenced regions and positions of the 29 genotyped SNPs and of the total 83 SNPs in the SP110 region are shown below.

Supplementary Figure 2. Linkage disequilibrium in the SP110 region.

LD between SP110 markers in the 48 CEU (2a and 2c) and 48 Russian (2b and 2d) subjects. Only markers with more than 10% minor allele frequency in both population samples are shown to simplify visual comparison. 2a and 2b - red squares indicate strong pairwise LD (high D’), white squares indicate no pairwise LD (low D’). Triangles indicate clusters of markers at high LD, suggesting presence of two LD blocks; polymorphisms show strong LD between each other within each block, but no LD is seen between polymorphisms in two different blocks. 2c and 2d – black squares indicate strong pairwise LD (r2=1), white squares indicate no pairwise LD (r2=0), grey squares indicate intermediate r2 values. Note the same location of the LD-breaking spot between rs7580900 and ss65624519 in the Russian and CEU samples.