Table 5.
Lead single-variant analysis results
| Region | Phenotype | Model | SNP | WGS/Chip N | CAF | WGS beta (SE) | WGS P | Chip beta (SE) | Chip P | Combined beta (SE) | Combined P |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2q12.1: IL18RAP | Avg desaturation | All | rs77375846 C | 4995, 4838 | 0.028–0.129 | −0.152 (0.049) | 1.87 × 10−3 | −0.264 (0.049) | 5.97 × 10−8 | −0.208 (0.035) | 1.57 × 10−9 |
| 2q33.3: PPIAP68 | Avg desaturation | All | rs60132122 T | 5222, 4838 | 0.308–0.637 | 0.062 (0.031) | 0.043 | 0.195 (0.034) | 6.26 × 10−9 | 0.122 (0.023) | 6.49 × 10−8 |
| 11q12.2: MS4A15 | Avg SpO2 | All | rs4939452 C | 7929, 13197 | 0.347–0.524 | 0.066 (0.023) | 4.34 × 10−3 | 0.063 (0.014) | 3.29 × 10−6 | 0.064 (0.012) | 4.87 × 10−8 |
| 18q12.3: LINC00907 | Avg SpO2 | All | rs187860354 G | 4500, 7391 | 0.006–0.022 | 0.442 (0.146) | 2.36 × 10−3 | 0.432 (0.097) | 8.53 × 10−6 | 0.436 (0.081) | 7.04 × 10−8 |
| 2q12.1: IL18RAP | Min SpO2 | All | rs138895820 G | 7705, 13194 | 0.025–0.131 | 0.510 (0.184) | 5.58 × 10−3 | 0.654 (0.128) | 3.36 × 10−7 | 0.607 (0.105) | 7.93 × 10−9 |
| 10p12.31: NEBL | Min SpO2 | Females | rs11453507 CA | 4450, 6202 | 0.138–0.514 | 0.651 (0.140) | 3.34 × 10−6 | 0.338 (0.102) | 8.63 × 10−4 | 0.446 (0.082) | 5.73 × 10−8 |
| 12q21.2: LINC024064 | Min SpO2 | Females | rs2176909 T | 4450, 6202 | 0.724–0.930 | 0.828 (0.157) | 1.38 × 10−7 | 0.319 (0.116) | 5.77 × 10−3 | 0.498 (0.093) | 9.06 × 10−8 |
| 5p13.3: C5orf22 | AHI | Males | rs10940956 A | 3502, 7043 | 0.470–0.759 | 0.930 (0.422) | 2.74 × 10−2 | 1.430 (0.269) | 1.09 × 10−7 | 1.285 (0.227) | 1.48 × 10−8 |
| 9p22.1: DENND4C | AHI | AA | rs111654000 A | 1717, 225 | 0.016–0.018 | −11.240 (2.268) | 7.18 × 10−7 | −18.110 (6.724) | 7.07 × 10−3 | −11.942 (2.149) | 2.74 × 10−8 |
| 1q31.2: AL954650.1 | AHI | AA | chr1:191965014_G/A A | 1717, 225 | 0.286–0.301 | 3.078 (0.641) | 1.56 × 10−6 | 5.080 (1.759) | 3.88 × 10−3 | 3.313 (0.602) | 3.75 × 10−8 |
| 8p12: AC068672.1, NRG1 | AHI | EA | rs35447033 T | 3246, 5095 | 0.060–0.094 | 2.247 (0.621) | 2.95 × 10−4 | 2.453 (0.521) | 2.54 × 10−6 | 2.368 (0.399) | 3.02 × 10−9 |
| 5p13.2: SLC45A2 | Avg SpO2 | EA | rs28777 A | 3201, 5024 | 0.885–0.969 | −0.526 (0.133) | 8.00 × 10−5 | −0.454 (0.096) | 2.23 × 10−6 | −0.478 (0.078) | 8.08 × 10−10 |
| 1q32.1: ATP2B4 | Avg SpO2 | HA | rs116133558 T | 2803, 7956 | 0.006–0.014 | 0.371 (0.120) | 2.08 × 10−3 | 0.294 (0.062) | 2.15 × 10−6 | 0.310 (0.055) | 1.88 × 10−8 |
| 1q23.3: intergenic (RNU6-755P) | Min SpO2 | HA | rs140743827 A | 2803, 7174 | 0.017–0.020 | −1.502 (0.593) | 1.13 × 10−2 | −1.770 (0.367) | 1.42 × 10−6 | −1.696 (0.312) | 5.51 × 10−8 |
| 1q32.1: ATP2B4 | Per90 | HA | rs116133558 T | 2803, 7956 | 0.006–0.014 | −1.005 (0.450) | 2.54 × 10−2 | −1.218 (0.207) | 4.15 × 10−9 | −1.181 (0.188) | 3.51 × 10−10 |
| 11p11.2: intergenic (AC104010.1) | Avg SpO2 | HA males | chr11:44652095_TC/T T | 1143, 3024 | 0.007–0.008 | 0.686 (0.248) | 5.65 × 10−3 | 0.710 (0.154) | 3.83 × 10−6 | 0.703 (0.131) | 7.25 × 10−8 |
| 10q22.1:HK1 | Min SpO2 | EA males | rs17476364 C | 1523, 3650 | 0.072–0.115 | 1.215 (0.392) | 1.94 × 10−3 | 1.099 (0.235) | 2.81 × 10−6 | 1.129 (0.201) | 2.01 × 10−8 |
| 8q23.2: KCNV1 | Min SpO2 | EA males | rs58365105 A | 1523, 3650 | 0.007–0.026 | −2.878 (0.864) | 8.65 × 10−4 | −2.406 (0.540) | 8.36 × 10−6 | −2.539 (0.458) | 2.96 × 10−8 |
| 2q35: AC019211.1 | Per90 | EA males | chr2:220369683_G/A A | 1540, 187 | 0.005–0.006 | 12.280 (2.431) | 4.38 × 10−7 | 17.505 (7.989) | 2.85 × 10−2 | 12.723 (2.326) | 4.48 × 10−8 |
Lead EMMAX single-variant associations within one order of magnitude of significance (combined p < 1.00 × 10−8) and with replication evidence (p < 0.05) are shown. Full results for all variants in each locus with p < 1.00 × 10−7, including additional associations with secondary models, and metadata and annotations, are provided in Additional file 1: Table S7