Appendix 1—table 2. Discovery stage GWAS for the UKBB cohort.
The information for B allele frequency (B Freq), odds-ratio (OR) and association (Beta; standard error of Beta; χ2 and P) were collected from the UKBB cohort. All genome-wide significant, LD-independent (r2 ≤0.3 pruned in order of UKBB association) SNPs that passed imputation QC are shown. SNPs with r2 = NA are the lead-SNPs of each distinct locus. The A and B alleles are on GRCh37 forward strand. OR was computed from SNP dosages and B as the effect allele. Rows are sorted by genomic position.
| rs-code | Chr | Position | A | B | r2 (reference SNP) |
B freq | OR | Beta | SE | χ2 | P |
|---|---|---|---|---|---|---|---|---|---|---|---|
| rs2235529 | 1 | 22450487 | C | T | NA | 0.157 | 1.14 | −0.005 | 5.81E-04 | 73.373 | 1.1E-17 |
| rs2092315 | 1 | 22507684 | C | T | 0.14 (rs2235529) |
0.248 | 1.07 | −0.003 | 4.90E-04 | 30.465 | 3.4E-08 |
| rs10929757 | 2 | 11702661 | A | C | NA | 0.579 | 1.08 | −0.003 | 4.32E-04 | 36.947 | 1.2E-09 |
| rs11674184 | 2 | 11721535 | T | G | 0.30 (rs10929757) |
0.386 | 0.94 | 0.002 | 4.36E-04 | 30.082 | 4.1E-08 |
| rs10936600 | 3 | 169514585 | A | T | NA | 0.244 | 0.91 | 0.003 | 4.91E-04 | 47.191 | 6.4E-12 |
| rs143835293 | 3 | 197623337 | A | G | NA | 0.002 | 1.75 | −0.043 | 6.33E-03 | 45.143 | 1.8E-11 |
| rs62323680 | 4 | 54546192 | G | A | NA | 0.067 | 1.16 | −0.006 | 8.49E-04 | 51.212 | 8.3E-13 |
| rs2202282 | 4 | 70634441 | C | T | NA | 0.497 | 1.07 | −0.003 | 4.22E-04 | 37.593 | 8.7E-10 |
| rs72709458 | 5 | 1283755 | C | T | NA | 0.206 | 1.12 | −0.004 | 5.28E-04 | 65.165 | 6.9E-16 |
| rs2736100 | 5 | 1286516 | C | A | 0.23 (rs72709458) | 0.498 | 0.91 | 0.003 | 4.23E-04 | 60.879 | 6.1E-15 |
| rs2853676 | 5 | 1288547 | T | C | 0.23 (rs2736100) | 0.731 | 0.91 | 0.003 | 4.77E-04 | 49.761 | 1.7E-12 |
| rs2456181 | 5 | 176450837 | C | G | NA | 0.484 | 1.07 | −0.002 | 4.24E-04 | 33.743 | 6.3E-09 |
| rs4870084 | 6 | 152543949 | C | T | 0.29 (rs6904757) | 0.189 | 0.92 | 0.003 | 5.44E-04 | 32.941 | 9.5E-09 |
| rs6928363 | 6 | 152546094 | G | A | 0.17 (rs58415480) | 0.485 | 0.92 | 0.003 | 4.24E-04 | 46.849 | 7.7E-12 |
| rs58415480 | 6 | 152562271 | C | G | NA | 0.155 | 1.18 | −0.007 | 5.89E-04 | 124.672 | 6.0E-29 |
| rs75510204 | 6 | 152592680 | T | G | 0.07 (rs58415480) | 0.012 | 1.29 | −0.012 | 2.07E-03 | 32.664 | 1.1E-08 |
| rs6904757 | 6 | 152593102 | A | G | 0.08 (rs6928363) | 0.363 | 0.93 | 0.003 | 4.42E-04 | 41.035 | 1.5E-10 |
| rs144444583 | 6 | 152684585 | T | C | 0.30 (rs58415480) | 0.128 | 1.12 | −0.004 | 6.37E-04 | 45.286 | 1.7E-11 |
| rs138821078 | 9 | 674217 | C | G | 0.13 (rs10975820) | 0.021 | 1.23 | −0.008 | 1.50E-03 | 31.819 | 1.7E-08 |
| rs10975820 | 9 | 684160 | G | A | 0.00 (rs7027685) | 0.142 | 1.12 | −0.004 | 6.08E-04 | 48.602 | 3.1E-12 |
| rs7027685 | 9 | 802228 | A | T | NA | 0.402 | 1.11 | −0.004 | 4.33E-04 | 75.424 | 3.8E-18 |
| rs114680331 | 9 | 815682 | T | C | 0.12 (rs7027685) | 0.100 | 1.11 | −0.004 | 7.21E-04 | 35.577 | 2.5E-09 |
| rs4742448 | 9 | 826585 | C | G | 0.28 (rs7027685) | 0.458 | 1.07 | −0.003 | 4.33E-04 | 33.714 | 6.4E-09 |
| rs2277163 | 9 | 827224 | A | G | 0.07 (rs7027685) | 0.947 | 0.87 | 0.005 | 9.51E-04 | 33.211 | 8.3E-09 |
| rs1265164 | 10 | 105674854 | A | G | NA | 0.869 | 0.91 | 0.004 | 6.27E-04 | 32.772 | 1.0E-08 |
| rs11246003 | 11 | 213723 | T | G | 0.00 (rs507139) | 0.044 | 0.85 | 0.006 | 1.03E-03 | 32.337 | 1.3E-08 |
| rs507139 | 11 | 225196 | G | A | NA | 0.074 | 0.84 | 0.006 | 8.11E-04 | 53.082 | 3.2E-13 |
| rs2207548 | 11 | 32368744 | C | A | 0.24 (rs10835889) | 0.423 | 1.09 | −0.003 | 4.30E-04 | 62.360 | 2.9E-15 |
| rs10835889 | 11 | 32370380 | G | A | NA | 0.159 | 1.14 | −0.005 | 5.81E-04 | 79.234 | 5.5E-19 |
| rs7120483 | 11 | 32406983 | G | C | 0.30 (rs10835889) | 0.120 | 1.12 | −0.004 | 6.51E-04 | 44.481 | 2.6E-11 |
| rs11031783 | 11 | 32459923 | C | A | 0.28 (rs10835889) | 0.204 | 1.09 | −0.003 | 5.25E-04 | 36.687 | 1.4E-09 |
| rs2553772 | 11 | 35085453 | T | G | NA | 0.538 | 1.07 | −0.002 | 4.24E-04 | 34.458 | 4.4E-09 |
| rs59021565 | 11 | 107999907 | C | G | 0.27 (rs141379009) | 0.091 | 1.11 | −0.004 | 7.38E-04 | 30.882 | 2.7E-08 |
| rs141379009 | 11 | 108149207 | T | G | NA | 0.027 | 1.32 | −0.011 | 1.30E-03 | 76.719 | 2.0E-18 |
| rs4988023 | 11 | 108168995 | A | C | 0.00 (rs141379009) | 0.144 | 0.89 | 0.004 | 6.01E-04 | 43.699 | 3.8E-11 |
| rs12223381 | 11 | 108354102 | C | T | 0.12 (rs59021565) | 0.406 | 1.07 | −0.002 | 4.31E-04 | 30.234 | 3.8E-08 |
| rs9669403 | 12 | 46798900 | G | A | 0.28 (rs12832777) | 0.402 | 1.07 | −0.003 | 4.35E-04 | 36.998 | 1.2E-09 |
| rs12832777 | 12 | 46831129 | T | C | NA | 0.701 | 1.09 | −0.003 | 4.61E-04 | 44.734 | 2.3E-11 |
| rs117245733 | 13 | 40723944 | G | A | 0.00 (rs7986407) | 0.016 | 1.26 | −0.010 | 1.74E-03 | 34.519 | 4.2E-09 |
| rs7986407 | 13 | 41179798 | A | G | NA | 0.310 | 1.09 | −0.003 | 4.56E-04 | 45.943 | 1.2E-11 |
| rs66998222 | 16 | 51481596 | G | A | NA | 0.201 | 0.91 | 0.003 | 5.28E-04 | 42.053 | 8.9E-11 |
| rs78378222 | 17 | 7571752 | T | G | NA | 0.013 | 1.53 | −0.020 | 1.93E-03 | 105.457 | 9.7E-25 |
| rs733381 | 22 | 40669648 | A | G | NA | 0.213 | 1.10 | −0.003 | 5.16E-04 | 42.919 | 5.7E-11 |
| rs5936989 | X | 70022420 | T | A | 0.27 (rs5937008) | 0.782 | 0.92 | 0.005 | 9.30E-04 | 32.606 | 1.1E-08 |
| rs5937008 | X | 70093038 | C | T | NA | 0.520 | 0.91 | 0.006 | 7.68E-04 | 65.570 | 5.6E-16 |
| rs7059898 | X | 70149078 | C | A | 0.27 (rs5937008) | 0.359 | 1.07 | −0.005 | 8.11E-04 | 31.756 | 1.7E-08 |
| rs7888560 | X | 131171122 | A | G | 0.19 (rs5930554) | 0.228 | 1.08 | −0.005 | 9.16E-04 | 31.830 | 1.7E-08 |
| rs5930554 | X | 131312089 | T | C | NA | 0.311 | 1.14 | −0.009 | 8.29E-04 | 107.076 | 4.3E-25 |
| rs5933158 | X | 131578034 | A | G | 0.21 (rs5930554) | 0.586 | 1.08 | −0.005 | 7.98E-04 | 38.833 | 4.6E-10 |
| rs5975338 | X | 131626317 | A | G | 0.28 (rs5930554) | 0.129 | 1.10 | −0.006 | 1.14E-03 | 32.201 | 1.4E-08 |