Table 1. Summary of association results and conditional logistic regression analysis of the 24 SNPs.
| MAFb | CLRAf | CLRAg | CLRAh | ||||||||||||||
| Gene | SNP | BP | Loction* | Distance# | LD& | Alleea | F_Ac | F_Ud | P value | Pe value | OR (95%CI) | OR | P value | OR | P value | OR | P value |
| HLA-G | rs35540400 | 29822923 | F*-3UTR | 24024 | 0 | T | 0.46 | 0.40 | 1.73E-04 | 0.608 | 1.32 (1.14-1.52) | 1.35 | 9.71E-05 | 1.35 | 1.01E-04 | 1.30 | 1.17E-03 |
| MICC | rs1264524 | 30404786 | F-5UTR | 17243 | 0 | A | 0.43 | 0.50 | 5.67E-05 | 0.199 | 0.74 (0.64-0.86) | 0.75 | 1.94E-04 | 0.76 | 2.74E-04 | 0.77 | 1.17E-03 |
| ITPR3 | rs3818528 | 33661091 | intron | / | 0 | G | 0.11 | 0.08 | 7.44E-04 | 1 | 1.52 (1.19-1.95) | 1.49 | 2.14E-03 | 1.49 | 2.24E-03 | 1.53 | 2.04E-03 |
| HLA-DPB2 | rs9277723 | 33091454 | intron | / | 0 | A | 0.39 | 0.46 | 7.54E-05 | 0.265 | 0.74 (0.64-0.86) | 0.73 | 6.00E-05 | 0.74 | 1.36E-04 | 0.79 | 3.49E-03 |
| IP6K3 | rs9469583 | 33717770 | F-5UTR | 3044 | 0 | A | 0.14 | 0.09 | 1.95E-04 | 0.685 | 1.53 (1.22-1.91) | 1.53 | 2.78E-04 | 1.51 | 4.44E-04 | 1.43 | 3.99E-03 |
| DDR1 | rs2517576 | 30815035 | F-5UTR | 35659 | 0.038 | A | 0.13 | 0.09 | 7.15E-04 | 1 | 1.47 (1.18-1.84) | 1.49 | 6.50E-04 | 1.44 | 1.67E-03 | 1.45 | 4.52E-03 |
| DDR1 | rs2844659 | 30824532 | F-5UTR | 26162 | 0.042 | A | 0.13 | 0.09 | 7.15E-04 | 1 | 1.47 (1.18-1.84) | 1.49 | 6.50E-04 | 1.44 | 1.67E-03 | 1.45 | 4.52E-03 |
| DDR1 | rs2844657 | 30829522 | F-5UTR | 21172 | 0.042 | G | 0.13 | 0.09 | 8.04E-04 | 1 | 1.47 (1.17-1.84) | 1.48 | 7.39E-04 | 1.44 | 1.86E-03 | 1.45 | 5.06E-03 |
| MLN | rs2281820 | 33768897 | coding | / | 0 | A | 0.19 | 0.14 | 1.39E-04 | 0.489 | 1.45 (1.20-1.76) | 1.43 | 3.24E-04 | 1.42 | 4.87E-04 | 1.35 | 5.14E-03 |
| HMGN4 | rs9379888 | 26526994 | F-5UTR | 11578 | 0 | A | 0.13 | 0.08 | 2.95E-05 | 0.104 | 1.67 (1.31-2.13) | 1.70 | 2.34E-05 | 1.69 | 3.10E-05 | 1.42 | 6.64E-03 |
| DPCR1 | rs11753326 | 30925985 | F-3UTR | 3987 | 0.034 | G | 0.13 | 0.09 | 6.25E-04 | 1 | 1.49 (1.18-1.87) | 1.48 | 9.54E-04 | 1.43 | 2.85E-03 | 1.39 | 1.11E-02 |
| HLA-DQA1 | rs9271300 | 32581582 | F-5UTR | 23587 | 0.015 | C | 0.45 | 0.51 | 2.26E-04 | 0.794 | 0.77 (0.67-0.88) | 0.84 | 2.76E-02 | 0.84 | 2.17E-02 | 0.84 | 3.46E-02 |
| NOTCH4 | rs482759 | 32195017 | F-5UTR | 3173 | 0.039 | G | 0.11 | 0.08 | 6.74E-04 | 1 | 1.52 (1.19-1.94) | 1.35 | 2.24E-02 | 1.31 | 3.88E-02 | 1.26 | 9.73E-02 |
| NOTCH4 | rs483574 | 32194956 | F-5UTR | 3112 | 0.039 | A | 0.11 | 0.08 | 6.74E-04 | 1 | 1.52 (1.19-1.94) | 1.35 | 2.24E-02 | 1.31 | 3.88E-02 | 1.26 | 9.73E-02 |
| C6orf100 | rs9257403 | 28916972 | F-3UTR | 4657 | 0.064 | G | 0.47 | 0.41 | 4.35E-04 | 1 | 1.29 (1.12-1.48) | 1.30 | 4.69E-04 | 1.20 | 1.81E-02 | 1.12 | 1.73E-01 |
| OR12D3 | rs9380120 | 29335537 | F-3UTR | 5663 | 0.782 | G | 0.08 | 0.12 | 1.49E-04 | 0.524 | 0.64 (0.51-0.81) | 0.65 | 3.38E-04 | 0.86 | 3.73E-01 | 0.82 | 2.46E-01 |
| C6orf100 | rs2071788 | 28912307 | 3UTR | / | 0.827 | A | 0.08 | 0.12 | 4.75E-04 | 1 | 0.67 (0.53-0.84) | 0.66 | 5.16E-04 | 1.44 | 2.49E-01 | 1.41 | 3.16E-01 |
| DDX6P1 | rs9357078 | 29297666 | 3UTR | / | 0.765 | A | 0.08 | 0.12 | 2.10E-04 | 0.738 | 0.65 (0.51-0.82) | 0.65 | 4.30E-04 | 0.88 | 4.39E-01 | 0.84 | 3.16E-01 |
| OR2B3 | rs4713201 | 29067263 | F-5UTR | 12173 | 0.529 | G | 0.09 | 0.13 | 7.64E-04 | 1 | 0.68 (0.54-0.85) | 0.68 | 1.45E-03 | 1.05 | 8.12E-01 | 1.02 | 9.29E-01 |
| OR2J3 | rs9295794 | 29104935 | F-3UTR | 24274 | 0.012 | A | 0.09 | 0.13 | 8.70E-04 | 1 | 0.68 (0.55-0.86) | 0.69 | 1.70E-03 | 1.04 | 8.23E-01 | 0.99 | 9.70E-01 |
| DPCR1 | rs2844695 | 30936014 | F-3UTR | 14016 | / | G | 0.38 | 0.45 | 7.60E-05 | 0.267 | 0.74 (0.64-0.86) | 0.72 | 2.27E-05 | 0.72 | 2.43E-05 | NA | NA |
| TRIM27 | rs3763338 | 28894311 | F-5UTR | 2543 | / | A | 0.10 | 0.14 | 1.62E-05 | 0.057 | 0.63 (0.50-0.78) | 0.62 | 2.15E-05 | NA | NA | NA | NA |
| HLA-DQA1 | rs35399661 | 32590990 | F-5UTR | 14179 | / | G | 0.13 | 0.08 | 6.07E-06 | 0.021 | 1.71 (1.36-2.17) | NA | NA | NA | NA | NA | NA |
| HLA-DQA1 | rs17533090 | 32590722 | F-5UTR | 14447 | / | A | 0.13 | 0.08 | 7.74E-06 | 0.027 | 1.70 (1.34-2.14) | NA | NA | NA | NA | NA | NA |
*Flanking;
#
the distance of the SNP to gene;
&
the LD (r2) of each SNP with the top SNP in HapMap;
a
effect allele;
b
Minor allele frequency;
c
Frequency of minor allele in cases;
d
Frequency of minor allele in controls;
e
Bonferroni corrected P value based on multiple testing of 3,515 SNPs;
Conditional regression analysis to (f) rs35399661, (g) rs35399661and rs3763338, and (h) rs35399661, rs3763338 and rs2844695.