Supplementary Table 2. Genotyped markers and association tests.

Marker / Alternative name / Position / Gene / Function / Marker type / Genotyping
method / MAF / TDT: P-value / Main effect: P-value / Comment
HLA-A / 30018310-30021632 / HLA-A / - / Gene / HLA-SBT / - / 2.9 x 10-7 / 0.012
rs762324 / 30563865 / HLA-E / promoter / SNP / SNPlex / 0.050 / 0.021 / 0.73
rs1059510 / 30565711 / HLA-E / syn / SNP / MassARRAY / 0.375 / 0.030 / 0.22
rs41560815 / 30566174 / HLA-E / syn / SNP / SNPlex / 0.000 / - / - / Monomorphic
rs41562314 / 30566193 / HLA-E / non-syn / SNP / SNPlex / 0.000 / - / - / Monomorphic
HLA-B / 31429630-31432914 / HLA-B / - / Gene / HLA-SBT / - / 3.7 x 10-26 / 5.2 x 10-3
rs2301747 / 31479566 / MICA / intron / SNP / SNPlex / 0.000 / - / - / Monomorphic
rs2523495 / 31485957 / MICA / intron / SNP / SNPlex / - / - / - / Mendelian errors
rs3828882 / 31487599 / MICA / intron / SNP / MassARRAY / 0.207 / 2.5 x 10-3 / 0.96
rs2256183 / 31488508 / MICA / intron / SNP / SNPlex / - / - / - / Mendelian errors
rs3132467 / 31488922 / MICA / intron / SNP / SNPlex / 0.322 / 5.1 x 10-8 / 0.090
rs2534671 / 31573640 / MICB / LR / SNP / SNPlex / 0.405 / 3.3 x 10-19 / 0.99
rs3134900 / 31581936 / MICB / coding / SNP / MassARRAY / 0.182 / 3.4 x 10-10 / 0.59
rs3131638 / 31583106 / MICB / intron / SNP / MassARRAY / 0.226 / 4.9 x 10-11 / 0.39
rs9281523 / BAT1NcoI RFLP / 31606224 / BAT1 / intron/LR / Indel / Fragment-length/RFLP / 0.208 / 2.9 x 10-12 / 0.67
rs1129640 / BAT1 +348/ +885 / 31614603 / BAT1 / syn / SNP / SNPlex / 0.177 / 1.2 x 10-4 / 0.90
rs34788230 / 31616432 / BAT1 / intron / Indel / Fragment-length / 0.295 / 9.1 x 10-16 / 0.60
rs6149515 / BAT1int1 / 31616459 / BAT1 / intron / Indel / Fragment-length / 0.031 / 4.5 x 10-4 / 0.56
rs3130059 / 31617263 / BAT1 / intron / SNP / SNPlex / 0.445 / 3.4 x 10-3 / 0.70
rs2239527 / BAT1 -22 / 31617758 / BAT1 / UTR / SNP / SNPlex / 0.443 / 2.5 x 10-3 / 0.45
rs41293919 / BAT1 -223 / 31617960 / BAT1 / UTR / SNP / MassARRAY / - / - / - / HWD
rs2239528 / BAT1 -348 / 31618084 / BAT1 / UTR / SNP / SNPlex / 0.234 / 5.6 x 10-7 / 0.44
rs3219186 / IKBL -421 / 31622960 / NFKBIL1 / promoter / Indel / Fragment-length / 0.163 / 1.6 x 10-8 / 0.85
rs2071592 / IKBL -63 / 31623319 / NFKBIL1 / promoter / SNP / SNPlex / 0.408 / 2.6 x 10-4 / 0.61
rs2857605 / 31632830 / NFKBIL1 / intron / SNP / SNPlex / 0.000 / - / - / Monomorphic
rs2230365 / IKBL +446 / 31633427 / NFKBIL1 / syn / SNP / SNPlex / 0.158 / 0.38 / 0.95
rs3130062 / IKBL +738 / 31633891 / NFKBIL1 / non-syn / SNP / TaqMan / 0.062 / 2.7 x 10-7 / 0.58
IKBL +1372* / 31634426 / NFKBIL1 / UTR / SNP / SNPlex / 0.000 / - / - / Monomorphic
rs1800683 / 31648050 / LTA / promoter / SNP / TaqMan / 0.438 / 1.5 x 10-4 / 0.91
rs909253 / LTA or TNFβNcoI RFLP/ +252/+249 / 31648292 / LTA / intron / SNP / SNPlex / 0.442 / 6.9 x 10-3 / 0.79
rs2229094 / 31648535 / LTA / non-syn / SNP / TaqMan / 0.272 / 0.039 / 0.84

Supplementary Table 2 (continued).

Marker / Alternative name / Position / Gene / Function / Marker type / Genotyping
method / MAF / TDT: P-value / Main effect: P-value / Comment
rs1041981 / LTA +265 / 31648763 / LTA / non-syn / SNP / TaqMan / 0.438 / 1.2 x 10-4 / 0.84
rs1799964 / TNF -1031 / 31650287 / LTA, TNF / promoter / SNP / SNPlex / 0.231 / 1.0 x 10-3 / 0.19
rs1800750 / TNF -376 / 31650942 / TNF / promoter / SNP / MassARRAY / 0.017 / 4.3 x 10-4 / 0.023
rs1800629 / TNF -308 / 31651010 / TNF / promoter / SNP / MassARRAY / 0.216 / 2.6 x 10-5 / 0.76
rs361525 / TNF -238 / 31651080 / TNF / promoter / SNP / SNPlex / 0.036 / 0.77 / 0.58
rs3093662 / TNF +851 / 31652168 / TNF / intron / SNP / SNPlex / 0.042 / 0.16 / 0.94
rs3132451 / 31690004 / AIF1 / promoter / SNP / SNPlex / 0.295 / 2.5 x 10-13 / 4.6 x 10-3
rs2857600 / 31690266 / AIF1 / promoter / SNP / MassARRAY / 0.091 / 4.4 x 10-14 / 0.48
rs2736182 / 31691291 / AIF1 / non-syn/LR/UTR / SNP / SNPlex / 0.011 / 0.10 / 0.34
rs2259571 / 31691806 / AIF1 / intron/UTR / SNP / TaqMan / 0.298 / 0.010 / 0.034
rs2269475 / 31691910 / AIF1 / non-syn/intron / SNP / SNPlex / 0.204 / 0.11 / 0.64
rs2227956 / 31886251 / HSPA1L / non-syn / SNP / SNPlex / 0.114 / 8.3 x 10-18 / 0.84
rs1043618 / 31891486 / HSPA1A / UTR / SNP / SNPlex / - / - / - / Low success rate
rs6457452 / HSPA1B -179 / 31903529 / HSPA1B / UTR / SNP / TaqMan / 0.027 / 0.88 / 0.084
rs3020644 / 32002605 / C2 / promoter / SNP / TaqMan / 0.387 / 0.92 / 0.46
rs7746553 / 32003952 / C2 / intron / SNP / SNPlex / 0.114 / 0.36 / 0.21
rs9332739 / 32011783 / C2 / non-syn / SNP / SNPlex / - / - / - / Bad clusters
rs4151666 / 32020837 / C2, CFB / intron/LR / SNP / SNPlex / - / - / - / Bad clusters
rs4151648 / 32021054 / C2, CFB / non-syn/LR / SNP / SNPlex / 0.000 / - / - / Monomorphic
rs4151667 / 32022003 / CFB / non-syn / SNP / SNPlex / 0.057 / 0.066 / 0.57
rs4151651 / 32023593 / CFB / non-syn / SNP / SNPlex / 0.050 / 0.44 / 0.92
rs537160 / 32024379 / CFB / intron / SNP / SNPlex / 0.439 / 0.50 / 0.82
rs1270942 / 32026839 / CFB / intron/LR / SNP / MassARRAY / 0.215 / 6.1 x 10-16 / 0.53
rs2072633 / 32027557 / CFB / intron/LR / SNP / SNPlex / 0.494 / 0.55 / 0.79
rs184003 / 32258274 / AGER / intron / SNP / MassARRAY / 0.051 / 0.26 / 0.081
rs2070600 / AGER +557 / 32259421 / AGER / non-syn/LR / SNP / SNPlex / 0.054 / 0.90 / 0.87
rs1800684 / 32259972 / AGER / syn/LR / SNP / SNPlex / 0.090 / 3.5 x 10-15 / 0.62
rs1800624 / AGER -374 / 32260365 / AGER / promoter / SNP / MassARRAY / 0.235 / 0.62 / 0.54
rs1800625 / AGER -429 / 32260420 / AGER / promoter / SNP / SNPlex / 0.250 / 3.5 x 10-10 / 0.87
rs2076530 / 32471794 / BTNL2 / non-syn / SNP / SNPlex / 0.467 / 7.9 x 10-3 / 0.35
rs9268480 / 32471822 / BTNL2 / syn / SNP / SNPlex / 0.354 / 1.1 x 10-9 / 0.78
rs2076523 / 32478813 / BTNL2 / splice site / SNP / SNPlex / 0.420 / 1.7 x 10-7 / 0.90
rs7192 / 32519624 / HLA-DRA / non-syn / SNP / SNPlex / 0.435 / 2.0 x 10-3 / 0.43
DRB1-DQA1-DQB1 / 32654525-32665540 / HLA-DRB1, DQA1 andDQB1 / - / Haplotypes / Various / - / 5.8 x 10-101 / -

Alternative name: marker name(s) used in literature. Positions are given on genome build 36. Function: syn and non-syn: synonymous and non-synonymous SNP, respectively, in protein-coding sequence; LR: locus-region (within 2 kb of transcribed sequence); UTR: untranslated region. MAF: minor allele frequency (calculated in founders); details of allele frequencies for HLA loci and the DRB1-DQA1-DQB1 haplotypes are available in Supplementary Table 3. TDT: transmission-disequilibrium test (uncorrected P-values). Main effect: conditional logistic regression adjusted for DRB1-DQA1-DQB1 genotypes. Comments about cause are given for markers that were excluded (HWD: Hardy-Weinberg disequilibrium). *Not referenced in dbSNP, but in Allcock (1999).1

Reference:

1.Allcock RJ, Christiansen FT & Price P. The central MHC gene IKBL carries a structural polymorphism that is associated with HLA-A3,B7,DR15. Immunogenetics 1999; 49(7-8): 660-665.