Table 2.
Meta-analysis results in the extended MHC I and MHC class II regions
| MGS Freqs | ----------------P-values---------------- | ----Odds Ratios---- | -----Information----- | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Rs ID | # | BP | A1/2 | Cont | Case | COMB | MGS | ISC | SGENE | MGS | ISC | SGENE | MGS | ISC | SGENE | Band | Gene(s) (location) |
| rs6939997 | 1 | 25929203 | T/C | 0.089 | 0.080 | 4.90E-07 | 1.40E-01 | 5.66E-04 | 2.85E-04 | 0.900 | 0.785 | 0.712 | 0.978 | 0.851 | 0.955 | 6p22.2 | SLC17A1 (intr) |
| rs13199775 | 2 | 25936761 | T/A | 0.087 | 0.075 | 1.19E-07 | 5.12E-02 | 5.66E-04 | 2.57E-04 | 0.869 | 0.785 | 0.710 | 0.999 | 0.851 | 0.956 | 6p22.2 | SLC17A1 (intr) |
| rs9461219 | 3 | 25944906 | G/C | 0.087 | 0.075 | 4.72E-07 | 4.99E-02 | 2.68E-03 | 2.52E-04 | 0.868 | 0.826 | 0.710 | 1.000 | 1.000 | 0.956 | 6p22.2 | SLC17A1 (up),SLC17A3 (dwn) |
| rs9467626 | 4 | 25981725 | A/C | 0.091 | 0.080 | 1.65E-07 | 5.32E-02 | 7.47E-04 | 2.68E-04 | 0.872 | 0.784 | 0.710 | 0.988 | 0.806 | 0.959 | 6p22.2 | SLC17A3 (intr) |
| rs2072806 | 5 | 26493072 | G/C | 0.115 | 0.097 | 9.27E-07 | 5.91E-03 | 2.80E-04 | 3.40E-02 | 0.836 | 0.814 | 0.857 | 0.959 | 1.000 | 0.971 | 6p22.1 | BTN3A2 (dwn),BTN2A2 (intr) |
| rs2072803 | 6 | 26500494 | C/G | 0.115 | 0.097 | 8.19E-07 | 5.53E-03 | 2.80E-04 | 3.23E-02 | 0.835 | 0.814 | 0.856 | 0.960 | 1.000 | 0.974 | 6p22.1 | BTN2A2 (intr bound),BTN3A1 (up) |
| rs6904071 | 7 | 27155235 | A/G | 0.186 | 0.166 | 1.78E-08 | 1.21E-02 | 3.03E-04 | 3.72E-04 | 0.879 | 0.819 | 0.799 | 0.987 | 0.851 | 0.988 | 6p22.1 | |
| rs926300 | 8 | 27167422 | T/A | 0.186 | 0.166 | 1.06E-08 | 1.22E-02 | 3.03E-04 | 2.08E-04 | 0.879 | 0.819 | 0.791 | 0.989 | 0.851 | 0.988 | 6p22.1 | |
| rs6913660 | 9 | 27199404 | A/C | 0.184 | 0.164 | 2.36E-08 | 1.71E-02 | 3.03E-04 | 3.35E-04 | 0.884 | 0.819 | 0.798 | 0.998 | 0.851 | 1.000 | 6p22.1 | HIST1H2AG (up),HIST1H2BJ (dwn) |
| rs13219181 | 10 | 27244204 | G/A | 0.183 | 0.163 | 1.29E-08 | 1.47E-02 | 3.03E-04 | 2.05E-04 | 0.881 | 0.819 | 0.791 | 0.983 | 0.851 | 0.989 | 6p22.1 | |
| rs13194053 | 11 | 27251862 | C/T | 0.182 | 0.162 | 9.54E-09 | 1.45E-02 | 3.03E-04 | 1.48E-04 | 0.880 | 0.819 | 0.783 | 0.977 | 0.851 | 0.978 | 6p22.1 | |
| rs13219354 | 12 | 27293643 | C/T | 0.118 | 0.102 | 1.12E-07 | 3.59E-02 | 5.11E-04 | 4.39E-04 | 0.877 | 0.823 | 0.766 | 0.994 | 1.000 | 1.000 | 6p22.1 | |
| rs3800307 | 13 | 27293771 | A/T | 0.205 | 0.183 | 4.35E-08 | 1.34E-02 | 3.35E-03 | 6.12E-05 | 0.886 | 0.880 | 0.787 | 1.000 | 1.000 | 0.988 | 6p22.1 | |
| rs13212921 | 14 | 27313401 | T/C | 0.124 | 0.108 | 1.28E-07 | 3.09E-02 | 5.76E-04 | 5.53E-04 | 0.873 | 0.823 | 0.770 | 0.960 | 0.940 | 0.968 | 6p22.1 | |
| rs4452638 | 15 | 27337244 | A/G | 0.117 | 0.102 | 2.68E-07 | 4.51E-02 | 3.96E-04 | 1.11E-03 | 0.882 | 0.821 | 0.780 | 1.000 | 1.000 | 0.987 | 6p22.1 | PRSS16 (dwn) |
| rs6938200 | 16 | 27339129 | G/A | 0.205 | 0.188 | 3.02E-07 | 5.28E-02 | 2.40E-03 | 1.51E-04 | 0.910 | 0.874 | 0.801 | 1.000 | 0.992 | 1.000 | 6p22.1 | PRSS16 (dwn) |
| rs6932590 | 17 | 27356910 | C/T | 0.240 | 0.215 | 7.13E-08 | 3.37E-03 | 2.23E-03 | 8.48E-04 | 0.872 | 0.877 | 0.834 | 0.973 | 0.933 | 1.000 | 6p22.1 | |
| rs3800316 | 18 | 27364081 | C/A | 0.257 | 0.229 | 3.81E-08 | 7.19E-04 | 3.51E-03 | 1.09E-03 | 0.856 | 0.886 | 0.834 | 0.975 | 0.956 | 0.977 | 6p22.1 | |
| rs7746199 | 19 | 27369303 | T/C | 0.185 | 0.160 | 5.03E-08 | 6.85E-04 | 8.77E-04 | 5.70E-03 | 0.837 | 0.859 | 0.839 | 1.000 | 1.000 | 1.000 | 6p22.1 | |
| rs3800318 | 20 | 27371620 | T/A | 0.180 | 0.158 | 6.38E-08 | 2.80E-03 | 8.82E-04 | 2.27E-03 | 0.855 | 0.859 | 0.822 | 0.998 | 1.000 | 0.981 | 6p22.1 | |
| rs16897515 | 21 | 27385999 | A/C | 0.173 | 0.154 | 1.83E-07 | 1.22E-02 | 6.40E-04 | 2.16E-03 | 0.876 | 0.853 | 0.816 | 1.000 | 1.000 | 0.972 | 6p22.1 | POM121L2 (missense) |
| rs13195040 | 22 | 27521903 | G/A | 0.087 | 0.076 | 2.50E-07 | 1.04E-01 | 3.00E-05 | 2.82E-03 | 0.892 | 0.714 | 0.768 | 1.000 | 1.000 | 0.983 | 6p22.1 | ZNF184 (dwn) |
| rs10484399 | 23 | 27642507 | G/A | 0.091 | 0.080 | 3.50E-07 | 1.09E-01 | 8.58E-06 | 8.69E-03 | 0.895 | 0.762 | 0.795 | 1.000 | 1.000 | 1.000 | 6p22.1 | |
| rs17693963 | 24 | 27818144 | C/A | 0.101 | 0.085 | 2.81E-07 | 2.87E-02 | 6.00E-05 | 8.85E-03 | 0.864 | 0.781 | 0.795 | 1.000 | 0.993 | 0.986 | 6p22.1 | |
| rs7776351 | 25 | 27834710 | T/C | 0.255 | 0.236 | 3.22E-07 | 2.83E-02 | 1.13E-04 | 6.51E-03 | 0.905 | 0.855 | 0.865 | 1.000 | 1.000 | 1.000 | 6p22.1 | |
| rs12182446 | 26 | 27853717 | A/G | 0.247 | 0.227 | 4.77E-07 | 2.99E-02 | 7.17E-05 | 1.22E-02 | 0.905 | 0.850 | 0.874 | 0.999 | 1.000 | 0.990 | 6p22.1 | |
| rs9272219 | --- | 32710247 | T/G | 0.283 | 0.263 | 6.88E-08 | 1.32E-02 | 2.24E-05 | 1.03E-02 | 0.897 | 0.847 | 0.880 | 1.000 | 1.000 | 0.977 | 6p21.32 | HLA-DQA1 (up) |
| rs9272535 | --- | 32714734 | A/G | 0.283 | 0.263 | 8.87E-08 | 1.63E-02 | 2.47E-05 | 9.92E-03 | 0.900 | 0.848 | 0.879 | 1.000 | 1.000 | 0.977 | 6p21.32 | HLA-DQA1 (intr) |
“#” refers to the numbering of SNPs in the LD diagram in Figure 1. “BP” = base pairs. “A1/2” = alleles 1 and 2 (minor/major, forward strand). “Freqs” = minor allele frequencies. “Cont” = controls, “Case” = cases. “COMB” = combined analysis (meta-analysis) of the three datasets. For SNP locations (as reported by snpper.chip.org): “intr”=intron; “up” = upstream (within 10 kb of transcribed sequence) and “dwn”=downstream (within 10 kb); “intr bound” = intron-exon boundary.
Shown are data for all SNPs with P < 10−6 in the extended MHC I and class II MHC regions of chromosome 6p, in the meta-analysis of European-ancestry MGS, ISC and SGENE data (see Table 1 and Supplementary Methods). Odds ratios are reported for the minor allele. Genome-wide significant meta-analysis P-values (P < 5x10−8) are shown in bold italics(see Supplementary Methods, p. S16, regarding this threshold). The information content for the SNP for each study is the imputation r2 reported by MACH 1.0 for MGS; and the PLINK and IMPUTE information measure for ISC and SGENE respectively; “1.000” indicates a SNP that was genotyped or had a perfect proxy. Genes within 10 kb of a SNP are listed; see Figure 1 for additional details for 6p22.1. See Supplementary Datafile 1 for additional meta-analysis results.