Appendix 4.
Top-ranked SNPs with p<0.01 from simple association testing with Rejectors (n=35) vs Non-Rejectors (n=42), all of whom are Caucasians
| MAF | MAF | MAF | REJ vs. NONREJ | REJ vs. CONTROLS | NONREJ vs. CONTROLS | |||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| SNP | rank | physical position | type | Closest gene | Distance to gene | Rejectors | Controls | Non-Rejectors | P-VALUE | OR | L95 | U95 | Chi-Sq P-value | OR | L95 | U95 | Chi-Sq P-value | OR | L95 | U95 |
| rs2975033 | 4 | 29930240 | INTERGENIC | HLA-G | 23348 | 36.36 | 25.62 | 14.86 | 0.0034 | 3.273 | 1.451 | 7.382 | 0.05727 | 1.659 | 0.9801 | 2.807 | 0.04007 | 0.5068 | 0.262 | 0.9804 |
| rs12206499 | 10 | 30045106 | INTERGENIC | HCG9 | −5765 | 36.36 | 25.69 | 16.22 | 0.0065 | 2.952 | 1.332 | 6.544 | 0.05914 | 1.653 | 0.9765 | 2.797 | 0.07133 | 0.5598 | 0.2957 | 1.06 |
| rs3823355 | 11 | 30050062 | UPSTREAM | HCG9 | −809 | 36.36 | 25.87 | 16.22 | 0.0065 | 2.952 | 1.332 | 6.544 | 0.06405 | 1.637 | 0.9675 | 2.77 | 0.06659 | 0.5545 | 0.2929 | 1.049 |
| rs6904029 | 12 | 30051046 | NON_SYNONYMOUS_CODING | HCG9 | 0 | 36.36 | 25.75 | 16.22 | 0.0065 | 2.952 | 1.332 | 6.544 | 0.06059 | 1.648 | 0.9738 | 2.788 | 0.06976 | 0.5581 | 0.2948 | 1.056 |
| rs2394255 | 2 | 30057800 | DOWNSTREAM | HCG9 | 3625 | 59.09 | 48.62 | 33.78 | 0.0027 | 2.831 | 1.423 | 5.631 | 0.1021 | 1.526 | 0.9166 | 2.542 | 0.01447 | 0.5391 | 0.3266 | 0.8901 |
| rs3869070 | 6 | 30131847 | INTRONIC | Q6ZU40_HUMAN | 0 | 56.25 | 44.75 | 32.43 | 0.0049 | 2.679 | 1.339 | 5.358 | 0.0755 | 1.587 | 0.9502 | 2.652 | 0.04098 | 0.5926 | 0.3572 | 0.9832 |
| rs9366752 | 1 | 30132656 | 3PRIME_UTR | C6orf12 | 0 | 33.33 | 20 | 12.16 | 0.0026 | 3.611 | 1.521 | 8.575 | 0.01061 | 2 | 1.165 | 3.433 | 0.1024 | 0.5538 | 0.27 | 1.136 |
| rs6909253 | 15 | 30163622 | INTERGENIC | RNF39 | 12015 | 54.55 | 37.25 | 32.43 | 0.0083 | 2.5 | 1.258 | 4.968 | 0.005529 | 2.021 | 1.22 | 3.35 | 0.4111 | 0.8086 | 0.4868 | 1.343 |
| rs9261394 | 16 | 30172541 | INTERGENIC | TRIM31 | −6114 | 54.55 | 38 | 32.43 | 0.0083 | 2.5 | 1.258 | 4.968 | 0.008155 | 1.958 | 1.181 | 3.245 | 0.344 | 0.7832 | 0.4716 | 1.301 |
| rs2523990 | 13 | 30185208 | INTRONIC | TRIM31 | 0 | 60.61 | 47.38 | 37.84 | 0.0071 | 2.527 | 1.278 | 4.997 | 0.0387 | 1.709 | 1.023 | 2.854 | 0.1156 | 0.6762 | 0.4143 | 1.104 |
| rs1345229 | 18 | 30290374 | UPSTREAM | TRIM26 | 1191 | 15.15 | 11.87 | 2.703 | 0.0086 | 6.429 | 1.354 | 30.53 | 0.4332 | 1.325 | 0.654 | 2.685 | 0.01625 | 0.2061 | 0.04976 | 0.8539 |
| rs9357097 | 7 | 30393100 | INTERGENIC | TRIM39 | −9500 | 15.15 | 30.95 | 36.11 | 0.0051 | 0.3159 | 0.1382 | 0.7224 | 0.006962 | 0.3984 | 0.1999 | 0.7937 | 0.3663 | 1.261 | 0.7619 | 2.087 |
| rs1264583 | 19 | 30401462 | UPSTREAM | TRIM39 | −1138 | 12.12 | 5 | 1.351 | 0.0095 | 10.07 | 1.224 | 82.82 | 0.01509 | 2.621 | 1.172 | 5.86 | 0.1556 | 0.2603 | 0.03527 | 1.921 |
| rs1264581 | 5 | 30405484 | SYNONYMOUS_CODING | TRIM39 | 0 | 14.06 | 5.29 | 1.351 | 0.0041 | 11.95 | 1.47 | 97.1 | 0.004299 | 2.93 | 1.356 | 6.329 | 0.1354 | 0.2453 | 0.03327 | 1.808 |
| rs3095150 | 17 | 31040511 | INTERGENIC | DPCR1 | 10534 | 45.45 | 42.8 | 24.32 | 0.0086 | 2.593 | 1.263 | 5.32 | 0.6759 | 1.114 | 0.6723 | 1.844 | 0.002013 | 0.4295 | 0.248 | 0.744 |
| rs6457699 | 3 | 33089625 | UPSTREAM | HLA-DOA | 4258 | 53.12 | 46.75 | 28.38 | 0.0031 | 2.86 | 1.414 | 5.786 | 0.3256 | 1.291 | 0.775 | 2.15 | 0.002381 | 0.4513 | 0.2672 | 0.7623 |
| rs9276994 | 8 | 33092233 | INTERGENIC | HLA-DOA | 6866 | 46.88 | 37.75 | 24.32 | 0.0055 | 2.745 | 1.332 | 5.658 | 0.1487 | 1.455 | 0.8726 | 2.426 | 0.02181 | 0.53 | 0.3058 | 0.9186 |
| rs6933994 | 14 | 33095098 | INTERGENIC | HLA-DOA | 9731 | 56.25 | 45.99 | 33.33 | 0.0072 | 2.571 | 1.282 | 5.156 | 0.7293 | 0.9134 | 0.5468 | 1.526 | 0.0007677 | 2.349 | 1.411 | 3.909 |
| rs9296068 | 9 | 33096673 | INTERGENIC | HLA-DOA | 11306 | 46.88 | 36.75 | 24.32 | 0.0055 | 2.745 | 1.332 | 5.658 | 0.1074 | 1.519 | 0.9105 | 2.533 | 0.0328 | 0.5532 | 0.3191 | 0.959 |
Parental Allele test and Gamete Competition (GC) test for the same snps as above
The 5′UTR flanking region of HLA-DOA is represented by 4 SNPs, of which rs6457699 lies roughly 4kb from the first HLA-DOA exon, and also shows differences in parental allele comparisons, which approach significance at p=0.055 (yellow cell).
rs9296068 is more frequent in parents of Rejectors, compared with parents of Non-Rejectors. However, differences are not statistically significant, due to reduced power in the Rejector group, and among Rejector parents, as a result of removing seven non-Caucasians, and adding 5 caucasian trios.