SupplementaryTable1.Primer sequences, amplicon product sizes and PCR conditions for the DNA amplification of five MHC class II POALIN loci
Alu name / Primer sequence(5'-3') / Fragment size (bp) / Annealing Tm(◦C) / ReferencesAbsent length / Present length
AluDPB2 / Forward / AGACTAAGGAGTGTGGATTTCTC / 422 / 754 / 60 / J. K. Kulski et al(2010)
AluDPB2 / Reverse / ACTTCTATCCTCCTCTTTCCTC / 422 / 754 / 60 / J. K. Kulski et al(2010)
AluDQA2-1 / Forward / CTGAAATCTTAATGTGGTTGG / 100 / 423 / 60 / J. K. Kulski et al(2010)
AluDQA2-1 / Reverse / GAGTAGAATAAGGAGAATTGC / 100 / 423 / 60 / J. K. Kulski et al(2010)
AluDQA2-2 / Forward / ATCCAGGCAGCCCCCAGGTATCA / 443 / 767 / 60 / This study
AluDQA2-2 / Reverse / CCTCGGCCTCCCAAAGTCCTGA / 443 / 767 / 60 / This study
AluDQA2-3 / Forward / TCAACAGGAGAATCAAAACCAG / 565 / 887 / 59 / This study
AluDQA2-3 / Reverse / ACCGTGTGAGCCAGGATG / 565 / 887 / 59 / This study
AluDQA1-1 / Forward / AACTTTAC[C/T]CATCTCTACCTCTC / 769 / 1082 / 60 / J. K. Kulski et al(2010)
AluDQA1-1 / Reverse / TGTTTCTCATACTTGACTGTGG / 769 / 1082 / 60 / J. K. Kulski et al(2010)
AluDQA1-2 / Forward / TGCCATGTAGCCTGGTCTA / 536 / 855 / 63 / J. K. Kulski et al(2010)
AluDQA1-2 / Reverse / CTGTCTTCATCTAGAGGTGT / 536 / 855 / 63 / J. K. Kulski et al(2010)
AluDQA1-3 / Forward / CATCTGTGGATTCAACCTACC / 248 / 561 / 57 / This study
AluDQA1-3 / Reverse / AAGCCCTGAGGTGGAAAT / 248 / 561 / 57 / This study
AluDRB1-1 / Forward / CACTAGTCAGTTCATCCTCTTGT / 474/424 / 763 / 60 / J. K. Kulski et al(2010)
AluDRB1-1 / Reverse / TATGTCTGTTG[G/T]AGATCTTGTG / 474/424 / 763 / 60 / J. K. Kulski et al(2010)
AluDRB1-2 / Forward / GAGGACTGGTGGGCATCA / 637/587 / 926 / 57 / This study
AluDRB1-2 / Reverse / AAATGCTTCCTTCTTGTTGTAAAT / 637/587 / 926 / 57 / This study
AluORF10-1 / Forward / AGGGATGAATAGCTTCCTGT / 136 / 459 / 63 / J. K. Kulski et al(2010)
AluORF10-1 / Reverse / GAATTGTCTTTGGATGGTGAG / 136 / 459 / 63 / J. K. Kulski et al(2010)
AluORF10-2 / Forward / ACAGTCCAGTGAATTGCCTATGAGAA / 299 / 622 / 55 / This study
AluORF10-2 / Reverse / TAGGGAGTAAGGAGAGGTGGAAGGA / 299 / 622 / 55 / This study
Note: the primers information were referred from Kulski JKet al.2010
SupplementaryTable2. The number of MHC class II Alu PCR product samples randomly selected for direct sequencing
Alulocus / Alu homozygous alleles *1 or *2
1,1 / 2,2
AluDPB2 / 11 / 4
AluDQA2 / 9 / -
AluDQA1 / 9 / 6
AluDRB1 / 9 / -
AluORF10 / 12 / 4
SupplementaryTable3.RepeatMasker annotated output file of repeat elements including Alu repeats detected within the sequenced PCR products of 64 randomly sequenced homozygous samples (Table S2) with Alu insertions (14 samples,allele*2) or no Alu insertions (50 samples, allele*1) at the five Alu loci within the MHC class II region (Fig. S1a).
ID / Perc / Perc / Perc / Query / Position in Query / Matching / Repeat / Position in Repeat / PCR productdiv. / del. / ins. / sequence / begin / end / (left) / repeat / class/family / begin / end / (left) / size bp
1 / 17.7 / 7.9 / 1.5 / s1.AluDPB2*2 / 89 / 151 / (565) / C / MER5A1 / DNA/hAT-Charlie / (57) / 109 / 43 / 754
2 / 0.9 / 0 / 0 / s1.AluDPB2*2 / 229 / 544 / (172) / + / AluYb8 / SINE/Alu / 1 / 316 / (2)
3 / 17.7 / 7.9 / 1.5 / s2.AluDPB2*2 / 92 / 154 / (559) / C / MER5A1 / DNA/hAT-Charlie / (57) / 109 / 43 / 754
4 / 0.9 / 0 / 0 / s2.AluDPB2*2 / 232 / 547 / (166) / + / AluYb8 / SINE/Alu / 1 / 316 / (2)
5 / 17.7 / 7.9 / 1.5 / s3.AluDPB2*2 / 93 / 155 / (577) / C / MER5A1 / DNA/hAT-Charlie / (57) / 109 / 43 / 754
6 / 0.9 / 0 / 0 / s3.AluDPB2*2 / 233 / 549 / (183) / + / AluYb8 / SINE/Alu / 1 / 317 / (1)
7 / 17.7 / 7.9 / 1.5 / s4.AluDPB2*2 / 88 / 150 / (576) / C / MER5A1 / DNA/hAT-Charlie / (57) / 109 / 43 / 754
8 / 0.9 / 0 / 0 / s4.AluDPB2*2 / 228 / 542 / (184) / + / AluYb8 / SINE/Alu / 1 / 315 / (3)
1 / 4.9 / 0 / 2 / s1.AluDQA1*2 / 61 / 364 / (175) / C / AluY / SINE/Alu / (13) / 298 / 1 / 855
2 / 19 / 2.5 / 0 / s1.AluDQA1*2 / 373 / 451 / (88) / + / MER2B / DNA/TcMar-Tigger / 247 / 327 / (9)
3 / 4.9 / 0 / 2 / s2.AluDQA1*2 / 60 / 363 / (173) / C / AluY / SINE/Alu / (13) / 298 / 1 / 855
4 / 19 / 2.5 / 0 / s2.AluDQA1*2 / 372 / 450 / (86) / + / MER2B / DNA/TcMar-Tigger / 247 / 327 / (9)
5 / 5.6 / 0 / 2 / s3.AluDQA1*2 / 62 / 367 / (172) / C / AluY / SINE/Alu / (11) / 300 / 1 / 855
6 / 20.7 / 2.3 / 0 / s3.AluDQA1*2 / 368 / 454 / (85) / + / MER2B / DNA/TcMar-Tigger / 239 / 327 / (9)
7 / 5 / 0 / 2 / s4.AluDQA1*2 / 59 / 361 / (176) / C / AluY / SINE/Alu / (14) / 297 / 1 / 855
8 / 19 / 2.5 / 0 / s4.AluDQA1*2 / 370 / 448 / (89) / + / MER2B / DNA/TcMar-Tigger / 247 / 327 / (9)
9 / 5.2 / 0 / 2 / s5.AluDQA1*2 / 45 / 349 / (170) / C / AluY / SINE/Alu / (12) / 299 / 1 / 855
10 / 20.7 / 2.3 / 0 / s5.AluDQA1*2 / 350 / 436 / (83) / + / MER2B / DNA/TcMar-Tigger / 239 / 327 / (9)
11 / 4.9 / 0 / 2 / s6.AluDQA1*2 / 61 / 364 / (175) / C / AluY / SINE/Alu / (13) / 298 / 1 / 855
12 / 19 / 2.5 / 0 / s6.AluDQA1*2 / 373 / 451 / (88) / + / MER2B / DNA/TcMar-Tigger / 247 / 327 / (9)
1 / 27.8 / 1 / 1.3 / s1.AluORF10*2 / 163 / 471 / (123) / C / AluYb9 / SINE/Alu / (10) / 308 / 1 / 622
2 / 29.1 / 1.3 / 1.6 / s2.AluORF10*2 / 164 / 472 / (116) / C / AluYb8 / SINE/Alu / (10) / 308 / 1 / 622
3 / 1.3 / 0 / 0.3 / s3.AluORF10*2 / 196 / 505 / (96) / C / AluYb8 / SINE/Alu / (9) / 309 / 1 / 622
4 / 1 / 0 / 0.3 / s4.AluORF10*2 / 196 / 506 / (96) / C / AluYb8 / SINE/Alu / (8) / 310 / 1 / 622
1 / 24.6 / 1.1 / 10.8 / s1.AluDPB2*1 / 65 / 155 / (238) / + / MER5A / DNA/hAT-Charlie / 85 / 167 / (22) / 422
2 / 31.1 / 4 / 3.5 / s10.AluDPB2*1 / 38 / 210 / (185) / C / MER5B / DNA/hAT-Charlie / (4) / 174 / 1 / 422
3 / 25.3 / 12.8 / 4.6 / s11.AluDPB2*1 / 39 / 179 / (220) / + / MER5B / DNA/hAT-Charlie / 27 / 178 / (0) / 422
4 / 24.6 / 1.1 / 10.8 / s2.AluDPB2*1 / 66 / 156 / (244) / + / MER5A / DNA/hAT-Charlie / 85 / 167 / (22) / 422
5 / 25.3 / 12.8 / 4.6 / s3.AluDPB2*1 / 40 / 180 / (218) / + / MER5B / DNA/hAT-Charlie / 27 / 178 / (0) / 422
6 / 31.1 / 4 / 3.5 / s4.AluDPB2*1 / 44 / 216 / (185) / C / MER5B / DNA/hAT-Charlie / (4) / 174 / 1 / 422
7 / 25.1 / 8.7 / 8.1 / s5.AluDPB2*1 / 43 / 215 / (187) / + / MER5B / DNA/hAT-Charlie / 5 / 178 / (0) / 422
8 / 24.6 / 1.1 / 10.8 / s6.AluDPB2*1 / 66 / 156 / (240) / + / MER5A / DNA/hAT-Charlie / 85 / 167 / (22) / 422
9 / 24.6 / 1.1 / 10.8 / s7.AluDPB2*1 / 98 / 188 / (207) / + / MER5A / DNA/hAT-Charlie / 85 / 167 / (22) / 422
10 / 25.1 / 8.7 / 8.1 / s8.AluDPB2*1 / 44 / 216 / (184) / + / MER5B / DNA/hAT-Charlie / 5 / 178 / (0) / 422
11 / 25.1 / 8.7 / 8.1 / s9.AluDPB2*1 / 39 / 211 / (188) / + / MER5B / DNA/hAT-Charlie / 5 / 178 / (0) / 422
1 / 20 / 2.9 / 0 / s1.AluDQA1*1 / 25 / 94 / (130) / + / MER2B / DNA/TcMar-Tigger / 243 / 314 / (22) / 536
2 / 20.3 / 2.7 / 0 / s2.AluDQA1*1 / 50 / 123 / (97) / + / MER2B / DNA/TcMar-Tigger / 239 / 314 / (22) / 536
3 / 21.8 / 2.3 / 0 / s3.AluDQA1*1 / 21 / 107 / (114) / + / MER2B / DNA/TcMar-Tigger / 239 / 327 / (9) / 536
4 / 21.6 / 2.7 / 0 / s4.AluDQA1*1 / 22 / 95 / (126) / + / MER2B / DNA/TcMar-Tigger / 239 / 314 / (22) / 536
5 / 18.9 / 2.7 / 0 / s5.AluDQA1*1 / 48 / 121 / (95) / + / MER2B / DNA/TcMar-Tigger / 239 / 314 / (22) / 536
6 / 20.3 / 2.7 / 0 / s6.AluDQA1*1 / 20 / 93 / (131) / + / MER2B / DNA/TcMar-Tigger / 239 / 314 / (22) / 536
7 / 21.8 / 2.3 / 0 / s7.AluDQA1*1 / 52 / 138 / (84) / + / MER2B / DNA/TcMar-Tigger / 239 / 327 / (9) / 536
8 / 18.9 / 2.7 / 0 / s8.AluDQA1*1 / 49 / 122 / (95) / + / MER2B / DNA/TcMar-Tigger / 239 / 314 / (22) / 536
9 / 20.3 / 2.7 / 0 / s9.AluDQA1*1 / 50 / 123 / (96) / + / MER2B / DNA/TcMar-Tigger / 239 / 314 / (22) / 536
1 / 24.5 / 0 / 0 / s1.AluDQA2*1 / 351 / 365 / (41) / + / AluSx / SINE/Alu / 121 / 135 / (177) / 443
2 / 9.8 / 0 / 0 / s2.AluDQA2*1 / 366 / 406 / (0) / + / Alu / SINE/Alu / 1 / 41 / (92) / 443
3 / 10.2 / 0 / 2 / s3.AluDQA2*1 / 358 / 407 / (4) / + / Alu / SINE/Alu / 1 / 49 / (84) / 443
4 / 11.3 / 0.3 / 2.2 / s8.AluDQA2*1 / 348 / 415 / (0) / + / FLAM_C / SINE/Alu / 1 / 52 / (81) / 443
5 / 12.8 / 0.3 / 2.2 / s9.AluDQA2*1 / 343 / 410 / (0) / + / FLAM_C / SINE/Alu / 1 / 52 / (81) / 443
There were no repetitive sequences detected in 4 sequenced samples of AluDQA2*1 / 443
There were no repetitive sequences detected in 9 sequenced samples of AluDRB1*1 / 424/474
There were no repetitive sequences detected in 12 sequenced samples of AluORF10*1 / 299
Note: An explanation of the headings within the Table are presented at
SupplementaryTable4.Hardy-Weinberg and Ewens-Watterson of the ten POALIN loci (P value)
HLA-Alu lociAluMICB / AluTF / AluHJ / AluHG / AluHF / AluDPB2 / AluDQA2 / AluDQA1 / AluDRB1 / AluORF10
Hardy-Weinberg / 0.614 / 1.000 / 0.296 / 0.751 / 1.000 / 0.461 / 1.000 / <0.05 / 0.804 / 0.451
Ewens-Watterson / 0.230 / 0.330 / 0.129 / 0.086 / 0.558 / 0.025 / 1.000 / 0.121 / 0.233 / 0.239
SupplementaryTable 5.The inferred ten-loci POALIN haplotypes in the MHC class I and class II regions of the Chinese Han (Frequency > 0.01)
AluDPB2 / AluDQA2 / AluDQA1 / AluDRB1 / AluORF10 / AluMICB / AluTF / AluHJ / AluHG / AluHF / frequency1 / 1 / 2 / 1 / 1 / 1 / 1 / 2 / 1 / 1 / 0.100
1 / 1 / 2 / 1 / 1 / 1 / 1 / 1 / 1 / 1 / 0.081
2 / 1 / 1 / 1 / 1 / 1 / 1 / 1 / 2 / 1 / 0.057
1 / 1 / 2 / 1 / 1 / 1 / 1 / 1 / 2 / 1 / 0.056
2 / 1 / 2 / 1 / 1 / 1 / 1 / 1 / 1 / 1 / 0.044
1 / 1 / 1 / 1 / 1 / 1 / 1 / 1 / 2 / 1 / 0.041
2 / 1 / 1 / 1 / 1 / 1 / 1 / 1 / 1 / 1 / 0.037
2 / 1 / 2 / 1 / 1 / 1 / 1 / 1 / 2 / 1 / 0.034
1 / 1 / 1 / 1 / 2 / 1 / 1 / 1 / 1 / 1 / 0.026
2 / 1 / 2 / 1 / 1 / 2 / 1 / 1 / 1 / 1 / 0.026
2 / 1 / 1 / 1 / 1 / 1 / 1 / 2 / 1 / 1 / 0.025
1 / 1 / 2 / 1 / 1 / 2 / 1 / 1 / 2 / 1 / 0.024
1 / 1 / 2 / 2 / 1 / 1 / 1 / 1 / 2 / 1 / 0.022
2 / 1 / 2 / 1 / 1 / 1 / 2 / 1 / 2 / 1 / 0.020
1 / 1 / 1 / 1 / 1 / 1 / 1 / 1 / 1 / 1 / 0.019
2 / 1 / 2 / 1 / 2 / 1 / 1 / 1 / 1 / 1 / 0.019
1 / 1 / 2 / 1 / 2 / 2 / 1 / 2 / 1 / 1 / 0.018
2 / 1 / 2 / 1 / 1 / 1 / 1 / 2 / 1 / 1 / 0.018
2 / 1 / 2 / 1 / 2 / 2 / 1 / 1 / 2 / 1 / 0.018
2 / 1 / 2 / 2 / 1 / 1 / 1 / 2 / 1 / 1 / 0.018
2 / 1 / 1 / 1 / 1 / 2 / 1 / 1 / 1 / 1 / 0.016
1 / 1 / 1 / 2 / 1 / 1 / 1 / 1 / 1 / 1 / 0.014
1 / 1 / 2 / 2 / 2 / 1 / 1 / 1 / 2 / 1 / 0.014
2 / 1 / 2 / 1 / 1 / 2 / 2 / 2 / 1 / 1 / 0.013
2 / 1 / 1 / 1 / 1 / 2 / 1 / 2 / 2 / 1 / 0.012
2 / 1 / 2 / 2 / 1 / 1 / 1 / 1 / 2 / 1 / 0.012
1 / 1 / 2 / 1 / 1 / 1 / 2 / 1 / 2 / 1 / 0.011
1 / 1 / 2 / 1 / 2 / 1 / 1 / 1 / 2 / 1 / 0.011
1 / 1 / 1 / 1 / 1 / 1 / 2 / 2 / 1 / 1 / 0.010
1 / 1 / 2 / 2 / 2 / 1 / 1 / 1 / 1 / 1 / 0.010
2 / 1 / 1 / 1 / 1 / 1 / 2 / 1 / 1 / 1 / 0.010
2 / 1 / 2 / 2 / 1 / 1 / 2 / 2 / 1 / 1 / 0.010
2 / 1 / 2 / 2 / 2 / 1 / 1 / 1 / 1 / 1 / 0.010
Supplementary Table 6. LD estimations (Wn) among five POALINs within MHC I region and HLA-A, HLA-B and HLA-C
Wn / AluMICB / HLA-B / HLA-C / AluTF / AluHJ / HLA-A / AluHG / AluHFAluMICB / 0.804* / 0.493* / 0.017 / 0.152* / 0.478* / 0.098 / 0.038
HLA-B / 0.704* / 0.542 / 0.559* / 0.644* / 0.552 / 0.630*
HLA-C / 0.379 / 0.365 / 0.403* / 0.432* / 0.489
AluTF / 0.038 / 0.295 / 0.073 / 0.057
AluHJ / 0.752* / 0.388* / 0.027
HLA-A / 0.851* / 0.467*
AluHG / 0.063
AluHF
Note: * means the p value < 0.01
SupplementaryTable 7.LD estimations (Wn) among five POALINs within MHC II region and HLA-DRB1.
Wn / AluDPB2 / AluDQA2 / AluDQA1 / AluDRB1 / HLA-DRB1 / AluORF10AluDPB2 / 0.048 / 0.087 / 0.034 / 0.434 / 0.126
AluDQA2 / 0.035 / 0.024 / 0.273 / 0.024
AluDQA1 / 0.215 / 0.817* / 0.143*
AluDRB1 / 0.818* / 0.204*
HLA-DRB1 / 0.673*
AluORF10
Note: * means the p value < 0.01
SupplementaryTable 8. Percentage association of the POALIN with particular HLA-A alleles in the POALIN/HLA class I haplotype pairs of
Chinese Han population
HLA-A / Frequency ofHLA allele / Frequency of
AluMICB*2 / % / Frequency of
AluTF*2 / % / Frequency of
AluHJ*2 / % / Frequency of
AluHG*2 / % / Frequency of
AluHF*2 / %
A*01:01 / 0.030 / 0.010 / 32.70 / 0.00 / 0.026 / 88.81 / 0.00 / 0.00
A*02:01 / 0.089 / 0.007 / 8.31 / 0.016 / 17.83 / 0.005 / 5.08 / 0.086 / 96.78 / 0.007 / 8.31
A*02:03 / 0.048 / 0.00 / 0.012 / 25.82 / 0.00 / 0.048 / 100.00 / 0.00
A*02:04 / 0.008 / 0.00 / 0.00 / 0.00 / 0.008 / 100.00 / 0.00
A*02:06 / 0.054 / 0.008 / 15.49 / 0.014 / 25.46 / 0.004 / 8.17 / 0.054 / 100.00 / 0.00
A*02:07 / 0.097 / 0.006 / 5.77 / 0.00 / 0.00 / 0.094 / 96.88 / 0.00
A*03:01 / 0.019 / 0.00 / 0.000 / 1.38 / 0.003 / 17.06 / 0.00 / 0.00
A*03:02 / 0.003 / 0.003 / 100.00 / 0.00 / 0.00 / 0.00 / 0.00
A*11:01 / 0.263 / 0.036 / 13.59 / 0.030 / 11.55 / 0.067 / 25.52 / 0.067 / 25.25 / 0.00
A*11:02 / 0.008 / 0.002 / 29.00 / 0.002 / 23.45 / 0.00 / 0.00 / 0.00
A*23:01 / 0.005 / 0.00 / 0.00 / 0.00 / 0.00 / 0.003 / 50.00
A*24:02 / 0.199 / 0.066 / 32.94 / 0.023 / 11.42 / 0.169 / 85.18 / 0.005 / 2.65 / 0.006 / 3.05
A*24:03 / 0.005 / 0.00 / 0.00 / 0.003 / 60.52 / 0.00 / 0.00
A*24:07 / 0.008 / 0.00 / 0.00 / 0.008 / 100.00 / 0.00 / 0.00
A*26:01 / 0.016 / 0.004 / 25.60 / 0.00 / 0.00 / 0.00 / 0.008 / 50.00
A*29:01 / 0.005 / 0.003 / 50.00 / 0.00 / 0.00 / 0.00 / 0.00
A*30:01 / 0.030 / 0.026 / 89.58 / 0.00 / 0.00 / 0.00 / 0.003 / 9.10
A*31:01 / 0.013 / 0.002 / 17.56 / 0.001 / 8.18 / 0.00 / 0.002 / 18.38 / 0.00
A*32:01 / 0.011 / 0.005 / 46.14 / 0.001 / 13.75 / 0.011 / 100.00 / 0.00 / 0.00
A*33:03 / 0.078 / 0.00 / 0.002 / 2.91 / 0.00 / 0.001 / 1.91 / 0.00
A*68:01 / 0.005 / 0.002 / 40.71 / 0.00 / 0.001 / 23.84 / 0.00 / 0.00
A*69:01 / 0.003 / 0.003 / 100.00 / 0.003 / 100.00 / 0.00 / 0.00 / 0.00
A*74:01 / 0.003 / 0.00 / 0.00 / 0.003 / 100.00 / 0.00 / 0.00
SupplementaryTable 9. Percentage association of the POALIN with particular HLA-B alleles in the POALIN/HLA class I haplotype pairs of
Chinese Han population
HLA-B / Frequency ofHLA allele / Frequency of
AluMICB*2 / % / Frequency of
AluTF*2 / % / Frequency of
AluHJ*2 / % / Frequency of
AluHG*2 / % / Frequency of
AluHF*2 / %
B*07:02 / 0.016 / 0.00 / 0.00 / 0.00 / 0.00 / 0.00
B*07:05 / 0.003 / 0.00 / 0.00 / 0.00 / 0.00 / 0.00
B*08:01 / 0.008 / 0.00 / 0.00 / 0.008 / 100.00 / 0.00 / 0.003 / 33.33
B*13:01 / 0.081 / 0.00 / 0.011 / 13.66 / 0.034 / 42.21 / 0.029 / 36.44 / 0.00
B*13:02 / 0.024 / 0.024 / 100.00 / 0.00 / 0.00 / 0.004 / 15.70 / 0.003 / 11.12
B*15:01 / 0.040 / 0.00 / 0.00 / 0.014 / 33.80 / 0.019 / 47.99 / 0.00
B*15:02 / 0.046 / 0.006 / 13.92 / 0.004 / 9.34 / 0.019 / 42.04 / 0.017 / 38.12 / 0.00
B*15:07 / 0.005 / 0.00 / 0.002 / 30.11 / 0.00 / 0.005 / 100.00 / 0.00
B*15:10 / 0.003 / 0.00 / 0.00 / 0.003 / 100.00 / 0.00 / 0.00
B*15:11 / 0.016 / 0.00 / 0.00 / 0.010 / 63.94 / 0.010 / 63.73 / 0.00
B*15:12 / 0.005 / 0.003 / 50.00 / 0.003 / 47.58 / 0.005 / 100.00 / 0.00 / 0.00
B*15:17 / 0.003 / 0.003 / 100.00 / 0.003 / 100.00 / 0.003 / 100.00 / 0.00 / 0.00
B*15:18 / 0.003 / 0.003 / 100.00 / 0.003 / 100.00 / 0.003 / 100.00 / 0.003 / 100.00 / 0.00
B*15:25 / 0.024 / 0.003 / 11.12 / 0.00 / 0.018 / 75.20 / 0.003 / 12.69 / 0.00
B*15:27: / 0.008 / 0.003 / 33.33 / 0.001 / 6.70 / 0.005 / 60.05 / 0.00 / 0.00
B*27:03 / 0.003 / 0.003 / 100.00 / 0.00 / 0.00 / 0.003 / 100.00 / 0.003 / 100.00
B*27:04 / 0.005 / 0.003 / 60.97 / 0.00 / 0.003 / 50.00 / 0.00 / 0.00
B*27:05 / 0.003 / 0.00 / 0.00 / 0.003 / 100.00 / 0.00 / 0.00
B*27:06 / 0.003 / 0.00 / 0.00 / 0.003 / 100.00 / 0.00 / 0.00
B*27:07 / 0.003 / 0.00 / 0.00 / 0.003 / 100.00 / 0.003 / 100.00 / 0.00
B*35:01 / 0.043 / 0.022 / 51.87 / 0.003 / 7.42 / 0.026 / 60.27 / 0.011 / 24.60 / 0.00
B*35:02 / 0.003 / 0.00 / 0.00 / 0.00 / 0.003 / 100.00 / 0.00
B*35:05 / 0.005 / 0.00 / 0.00 / 0.003 / 50.00 / 0.00 / 0.00
B*35:10 / 0.003 / 0.00 / 0.003 / 100.00 / 0.00 / 0.003 / 100.00 / 0.00
B*37:01 / 0.005 / 0.003 / 50.00 / 0.00 / 0.003 / 50.00 / 0.00 / 0.002 / 38.36
B*38:02 / 0.030 / 0.003 / 9.27 / 0.00 / 0.009 / 30.17 / 0.019 / 62.94 / 0.003 / 9.10
B*39:01 / 0.013 / 0.00 / 0.003 / 20.01 / 0.005 / 38.96 / 0.007 / 55.51 / 0.00
B*40:01 / 0.118 / 0.00 / 0.026 / 22.15 / 0.029 / 24.22 / 0.046 / 38.85 / 0.003 / 2.55
B*40:02 / 0.011 / 0.003 / 25.02 / 0.00 / 0.004 / 38.79 / 0.00 / 0.00
B*40:06 / 0.019 / 0.003 / 16.48 / 0.005 / 25.93 / 0.006 / 34.08 / 0.013 / 66.79 / 0.003 / 15.89
B*44:02 / 0.011 / 0.00 / 0.003 / 25.02 / 0.00 / 0.00 / 0.00
B*44:03 / 0.032 / 0.008 / 24.09 / 0.00 / 0.00 / 0.00 / 0.00
B*46:01 / 0.151 / 0.00 / 0.003 / 2.08 / 0.005 / 3.41 / 0.103 / 68.73 / 0.00
B*47:01 / 0.003 / 0.00 / 0.00 / 0.003 / 100.00 / 0.00 / 0.003 / 100.00
B*48:01 / 0.022 / 0.022 / 100.00 / 0.006 / 30.13 / 0.011 / 50.00 / 0.012 / 54.39 / 0.00
B*48:03 / 0.003 / 0.003 / 100.00 / 0.00 / 0.00 / 0.003 / 100.00 / 0.00
B*49:01 / 0.003 / 0.00 / 0.00 / 0.00 / 0.00 / 0.00
B*50:01 / 0.005 / 0.00 / 0.00 / 0.00 / 0.00 / 0.00
B*51:01 / 0.038 / 0.00 / 0.024 / 62.90 / 0.007 / 19.45 / 0.024 / 63.83 / 0.00
B*51:02 / 0.005 / 0.005 / 100.00 / 0.00 / 0.00 / 0.00 / 0.00
B*52:01 / 0.027 / 0.00 / 0.001 / 4.35 / 0.004 / 16.67 / 0.007 / 27.12 / 0.003 / 10.01
B*52:06 / 0.003 / 0.00 / 0.00 / 0.003 / 100.00 / 0.00 / 0.00
B*54:01 / 0.043 / 0.036 / 84.77 / 0.00 / 0.023 / 53.82 / 0.00 / 0.00
B*55:02 / 0.030 / 0.015 / 49.81 / 0.00 / 0.010 / 32.30 / 0.011 / 37.44 / 0.00
B*56:01 / 0.003 / 0.00 / 0.00 / 0.00 / 0.00 / 0.00
B*56:02 / 0.003 / 0.00 / 0.00 / 0.00 / 0.00 / 0.00
B*57:01 / 0.008 / 0.008 / 100.00 / 0.00 / 0.008 / 100.00 / 0.003 / 33.33 / 0.00
B*58:01 / 0.051 / 0.003 / 5.32 / 0.00 / 0.005 / 8.83 / 0.00 / 0.00
B*67:01 / 0.003 / 0.00 / 0.00 / 0.00 / 0.00 / 0.003 / 100.00
B*78:01 / 0.005 / 0.00 / 0.003 / 50.00 / 0.003 / 50.00 / 0.003 / 50.00 / 0.00
B*78:02 / 0.003 / 0.00 / 0.00 / 0.003 / 100.00 / 0.003 / 100.00 / 0.00
SupplementaryTable 10. Percentage association of the POALIN with particular HLA-Calleles in the POALIN/HLA class I haplotype pairs of
Chinese Han population
HLA-Cw / Frequency ofHLA allele / Frequency of
AluMICB*2 / % / Frequency of
AluTF*2 / % / Frequency of
AluHJ*2 / % / Frequency of
AluHG*2 / % / Frequency of
AluHF*2 / %
C*01:02 / 0.215 / 0.042 / 19.56 / 0.008 / 3.89 / 0.047 / 21.79 / 0.114 / 53.20 / 0.00
C*01:03 / 0.003 / 0.00 / 0.00 / 0.003 / 100.00 / 0.003 / 100.00 / 0.003 / 100.00
C*03:02 / 0.056 / 0.00 / 0.007 / 12.22 / 0.005 / 7.97 / 0.00 / 0.00
C*03:03 / 0.065 / 0.025 / 38.01 / 0.007 / 11.38 / 0.033 / 50.78 / 0.014 / 22.41 / 0.00
C*03:04 / 0.110 / 0.00 / 0.020 / 18.50 / 0.032 / 29.12 / 0.035 / 31.75 / 0.004 / 3.25
C*03:07 / 0.003 / 0.003 / 100.00 / 0.00 / 0.003 / 100.00 / 0.00 / 0.00
C*04:01 / 0.062 / 0.017 / 27.20 / 0.006 / 9.64 / 0.037 / 59.81 / 0.014 / 22.57 / 0.00
C*04:03 / 0.038 / 0.012 / 30.61 / 0.00 / 0.024 / 64.48 / 0.007 / 18.36 / 0.003 / 7.15
C*05:01 / 0.003 / 0.00 / 0.00 / 0.003 / 100.00 / 0.00 / 0.003 / 100.00
C*05:04 / 0.008 / 0.00 / 0.001 / 13.75 / 0.00 / 0.00 / 0.00
C*05:11 / 0.003 / 0.003 / 100.00 / 0.00 / 0.00 / 0.003 / 100.00 / 0.00
C*06:02 / 0.043 / 0.031 / 71.77 / 0.00 / 0.008 / 18.48 / 0.00 / 0.005 / 12.51
C*06:04 / 0.003 / 0.003 / 100.00 / 0.00 / 0.00 / 0.00 / 0.00
C*07:01 / 0.030 / 0.001 / 4.97 / 0.008 / 26.34 / 0.00 / 0.021 / 69.53 / 0.00
C*07:02 / 0.156 / 0.011 / 7.16 / 0.00 / 0.046 / 29.52 / 0.065 / 41.73 / 0.010 / 6.32
Cw07:04 / 0.003 / 0.00 / 0.00 / 0.003 / 100.00 / 0.003 / 100.00 / 0.00
C*08:01 / 0.032 / 0.011 / 34.90 / 0.005 / 15.13 / 0.013 / 41.23 / 0.010 / 30.48 / 0.00
C*08:04 / 0.043 / 0.019 / 43.46 / 0.012 / 27.73 / 0.012 / 28.46 / 0.031 / 72.98 / 0.00
C*12:02 / 0.027 / 0.005 / 17.11 / 0.003 / 9.64 / 0.008 / 31.21 / 0.006 / 21.24 / 0.00
C*12:03 / 0.022 / 0.00 / 0.00 / 0.004 / 20.50 / 0.005 / 25.38 / 0.00
C*12:14 / 0.003 / 0.00 / 0.00 / 0.00 / 0.003 / 100.00 / 0.00
C*14:02 / 0.046 / 0.00 / 0.017 / 37.96 / 0.013 / 28.95 / 0.026 / 57.86 / 0.00
C*14:06 / 0.003 / 0.00 / 0.003 / 100.00 / 0.00 / 0.00 / 0.00
C*15:02 / 0.024 / 0.002 / 7.28 / 0.008 / 31.21 / 0.007 / 30.29 / 0.006 / 23.47 / 0.00
C*15:04 / 0.003 / 0.00 / 0.00 / 0.00 / 0.00 / 0.00
SupplementaryTable11. Percentage association of the POALIN with particular HLA-DRB1 alleles in the POALIN/HLA class II haplotype pairs of
Chinese Han population
HLA-DRB1 / AluDPB2*2 / % / AluDQA2*2 / % / AluDQA1*2 / % / AluDRB1*2 / % / AluORF10*2 / %DRB1*01:01 / 0.024 / 0.006 / 22.86 / 0.00 / 0.016 / 66.68 / 0.024 / 100.00 / 0.001 / 5.99
DRB1*03:01 / 0.035 / 0.007 / 20.95 / 0.00 / 0.003 / 8.01 / 0.001 / 2.89 / 0.018 / 52.19
DRB1*03:05 / 0.003 / 0.00 / 0.00 / 0.00 / 0.00 / 0.003 / 100.00
DRB1*04:01 / 0.003 / 0.003 / 100.00 / 0.00 / 0.003 / 100.00 / 0.003 / 100.00 / 0.00
DRB1*04:02 / 0.003 / 0.003 / 100.00 / 0.00 / 0.003 / 100.00 / 0.00 / 0.00
DRB1*04:03 / 0.016 / 0.008 / 51.95 / 0.00 / 0.016 / 100.00 / 0.00 / 0.00
DRB1*04:04 / 0.003 / 0.003 / 100.00 / 0.00 / 0.003 / 100.00 / 0.00 / 0.00
DRB1*04:05 / 0.059 / 0.026 / 44.15 / 0.00 / 0.059 / 100.00 / 0.008 / 12.75 / 0.050 / 84.41
DRB1*04:06 / 0.027 / 0.017 / 61.83 / 0.00 / 0.027 / 100.00 / 0.00 / 0.003 / 10.42
DRB1*04:10 / 0.008 / 0.008 / 100.00 / 0.00 / 0.008 / 100.00 / 0.00 / 0.005 / 64.27
DRB1*07:01 / 0.062 / 0.018 / 29.78 / 0.00 / 0.054 / 86.62 / 0.00 / 0.00
DRB1*08:02 / 0.008 / 0.003 / 33.33 / 0.00 / 0.008 / 100.00 / 0.00 / 0.003 / 33.33
DRB1*08:03 / 0.089 / 0.037 / 41.51 / 0.00 / 0.012 / 13.75 / 0.006 / 6.37 / 0.003 / 3.26
DRB1*08:27 / 0.003 / 0.00 / 0.00 / 0.00 / 0.00 / 0.00
DRB1*09:01 / 0.159 / 0.094 / 58.98 / 0.00 / 0.150 / 94.72 / 0.006 / 3.47 / 0.005 / 3.20
DRB1*09:09 / 0.003 / 0.00 / 0.00 / 0.003 / 100.00 / 0.00 / 0.00
DRB1*10:01 / 0.003 / 0.00 / 0.00 / 0.00 / 0.00 / 0.00
DRB1*11:01 / 0.054 / 0.041 / 75.49 / 0.00 / 0.006 / 10.45 / 0.00 / 0.004 / 7.55
DRB1*11:04 / 0.008 / 0.008 / 100.00 / 0.00 / 0.00 / 0.00 / 0.00
DRB1*11:31 / 0.003 / 0.00 / 0.00 / 0.00 / 0.00 / 0.00
DRB1*11:52 / 0.003 / 0.003 / 100.00 / 0.00 / 0.00 / 0.00 / 0.00
DRB1*12:01 / 0.011 / 0.00 / 0.00 / 0.00 / 0.00 / 0.00
DRB1*12:02 / 0.164 / 0.058 / 35.38 / 0.00 / 0.153 / 93.33 / 0.008 / 4.80 / 0.010 / 6.31
DRB1*12:19 / 0.003 / 0.00 / 0.00 / 0.00 / 0.00 / 0.003 / 100.00
DRB1*13:01 / 0.011 / 0.00 / 0.00 / 0.003 / 25.49 / 0.00 / 0.00
DRB1*13:02 / 0.038 / 0.016 / 42.40 / 0.00 / 0.007 / 19.16 / 0.003 / 7.23 / 0.00
DRB1*13:28 / 0.003 / 0.003 / 100.00 / 0.00 / 0.00 / 0.00 / 0.00
DRB1*14:01 / 0.027 / 0.021 / 78.39 / 0.00 / 0.016 / 60.01 / 0.005 / 20.39 / 0.003 / 10.60
DRB1*14:02 / 0.003 / 0.003 / 100.00 / 0.00 / 0.00 / 0.00 / 0.00
DRB1*14:03 / 0.008 / 0.008 / 100.00 / 0.00 / 0.00 / 0.00 / 0.00
DRB1*14:04 / 0.005 / 0.005 / 100.00 / 0.00 / 0.00 / 0.00 / 0.00
DRB1*14:05 / 0.008 / 0.008 / 100.00 / 0.00 / 0.005 / 66.67 / 0.00 / 0.00
DRB1*14:07 / 0.003 / 0.00 / 0.00 / 0.00 / 0.00 / 0.00
DRB1*14:32 / 0.005 / 0.003 / 50.00 / 0.00 / 0.003 / 50.00 / 0.00 / 0.00
DRB1*14:35 / 0.003 / 0.00 / 0.00 / 0.00 / 0.00 / 0.00
DRB1*15:01 / 0.073 / 0.032 / 43.46 / 0.00 / 0.070 / 96.22 / 0.064 / 88.51 / 0.039 / 53.40
DRB1*15:02 / 0.035 / 0.008 / 23.46 / 0.003 / 7.70 / 0.035 / 100.00 / 0.027 / 75.88 / 0.009 / 24.50
DRB1*15:04 / 0.008 / 0.00 / 0.00 / 0.008 / 100.00 / 0.008 / 100.00 / 0.003 / 33.33
DRB1*16:02 / 0.022 / 0.012 / 57.74 / 0.00 / 0.019 / 86.33 / 0.019 / 86.61 / 0.014 / 64.42
SupplementaryTable 12. Percentage association between HLA-DRB1 alleles and the Alu class II POALIN
DRB1 allele / AluDPB2 / AluDQA2 / AluDQA1 / AluDRB1 / AluORF10Caucasian / Japanese / Han / Caucasian / Japanese / Han / Caucasian / Japanese / Han / Caucasian / Japanese / Han / Caucasian / Japanese / Han
DRB1*01 / 59.0 / 81.3 / 22.9 / 15.7 / 6.3 / 2.4 / 66.7 / 100.0 / 75.0 / 100.0 / 12.3 / 6.3 / 6.0
DRB1*03 / 35.1 / 19.5 / 76.0 / 7.4 / 2.7 / 1.6 / 55.6
DRB1*04 / 29.2 / 59.9 / 56.8 / 1.6 / 92.3 / 73.5 / 100.0 / 4.6 / 2.2 / 8.7 / 3.5 / 53.1 / 49.0
DRB1*07 / 51.6 / 29.8 / 17.4 / 100.0 / 86.6 / 62.0
DRB1*08 / 3.0 / 50.1 / 39.7 / 54.2 / 100.0 / 24.1 / 20.4 / 4.8 / 5.7 / 5.6
DRB1*09 / 74.8 / 57.0 / 58.0 / 29.1 / 100.0 / 79.9 / 94.8 / 3.4 / 24.0 / 3.1
DRB1*10 / 100.0 / 98.3 / 100.0 / 49.6
DRB1*11 / 33.0 / 76.4 / 3.5 / 8.4 / 6.0
DRB1*12 / 65.3 / 32.7 / 77.8 / 86.3 / 4.4 / 7.4
DRB1*13 / 38.0 / 36.5 / 35.6 / 2.5 / 19.5 / 5.3 / 10.2
DRB1*14 / 66.9 / 43.6 / 77.6 / 8.1 / 39.1 / 8.9 / 4.6
DRB1*15 / 63.7 / 27.4 / 34.4 / 2.3 / 100.0 / 77.1 / 97.6 / 100.0 / 82.6 / 85.5 / 89.1 / 43.3
DRB1*16 / 59.7 / 57.7 / 20.1 / 100.0 / 100.0 / 86.3 / 100.0 / 100.0 / 86.6 / 100.0 / 64.4
Note: The data of five POALINs within MHC II region in Japanese and Caucasian were published previously (Kulski JKet al.2010).
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