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Table 5 Lead single-variant analysis results

From: Whole-genome association analyses of sleep-disordered breathing phenotypes in the NHLBI TOPMed program

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
  1. 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