Extended Data Table 2.
Low-frequency variants associated with adult height.59 variants (51 missense or nonsense) with minor allele frequency between 1 and 5% in European-ancestry participants that have Pcombined<2×10-7. For TTN-rs16866412 and NOL8-rs921122, the association is significant (P<2×10-7) upon conditional analysis. The direction of the effect (Beta, standard deviation units) and effect allele frequency (AF) is given for the alternate (Alt) allele. For each variant, we provide the most severe annotation using the ENSEMBL Variant Effect Predictor (VEP) tool. N, sample size; Ref, reference allele; SE, standard error
| Discovery (N up to 381,625) | Validation (N up to 252,501) | Combined N up to 634,126) | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Variant | Chr:Pos | Ref/Alt | Gene | Annotation | AF | Beta | SE | P-value | AF | Beta | SE | P-value | AF | Beta | SE | P-value |
| rs41292521 | 1:51873967 | G/A | EPS15 | missense | 0.020 | 0.045 | 0.008 | 5.07E-08 | 0.023 | 0.065 | 0.010 | 7.60E-11 | 0.021 | 0.053 | 0.006 | 2.56E-17 |
| rs61730011 | 1:119427467 | A/C | TBX15 | missense | 0.042 | -0.059 | 0.006 | 1.61E-24 | 0.046 | -0.056 | 0.007 | 4.19E-15 | 0.044 | -0.058 | 0.005 | 2.79E-36 |
| rsl1580946 | 1:150551327 | G/A | MCLl | missense | 0.014 | 0.061 | 0.010 | 2.16E-09 | 0.015 | 0.085 | 0.012 | 7.86E-12 | 0.015 | 0.070 | 0.008 | 1.55E-19 |
| rs141845046 | 1:154987704 | c/t | ZBTB7B | missense | 0.028 | 0.058 | 0.007 | 7.30E-17 | 0.025 | 0.061 | 0.010 | 4.46E-10 | 0.027 | 0.059 | 0.006 | 3.46E-25 |
| rs79485039 | 1:180886140 | C/T | KIAA1614 | missense | 0.026 | 0.034 | 0.007 | 1.41E-06 | 0.031 | 0.030 | 0.009 | 4.51E-04 | 0.028 | 0.033 | 0.006 | 2.63E-09 |
| rs52826764 | 2:20205541 | C/T | MATN3 | missense | 0.026 | -0.071 | 0.007 | 2.67E-23 | 0.028 | -0.084 | 0.010 | 6.60E-19 | 0.027 | -0.076 | 0.006 | 3.74E-41 |
| rs16859517 | 2:219949184 | C/T | NHEJ1 | intron | 0.036 | 0.059 | 0.006 | 5.96E-21 | 0.036 | 0.064 | 0.008 | 1.12E-15 | 0.036 | 0.061 | 0.005 | 8.20E-37 |
| rsl6866412 | 2:179474668 | G/A | TTN | missense | 0.013 | -0.053 | 0.010 | 1.35E-07 | 0.010 | -0.019 | 0.015 | 2.15E-01 | 0.012 | -0.042 | 0.008 | 3.44E-07 |
| rs7571816 | 2:233077064 | A/G | DIS3L2 | intron | 0.025 | -0.060 | 0.007 | 2.35E-16 | 0.023 | -0.079 | 0.010 | 2.58E-15 | 0.024 | -0.066 | 0.006 | 6.46E-31 |
| rs2229089 | 3:14214524 | G/A | XPC | missense | 0.031 | -0.038 | 0.007 | 1.22E-08 | 0.035 | -0.020 | 0.008 | 1.68E-02 | 0.033 | -0.030 | 0.005 | 1.29E-08 |
| rs76208147 | 3:47162886 | C/T | SETD2 | missense | 0.019 | 0.048 | 0.009 | 2.24E-08 | 0.016 | 0.062 | 0.012 | 2.22E-07 | 0.018 | 0.053 | 0.007 | 1.65E-13 |
| rs35713889 | 3:49162583 | C/T | LAMB2 | missense | 0.039 | 0.043 | 0.006 | 3.28E-12 | 0.045 | 0.060 | 0.007 | 1.33E-16 | 0.041 | 0.050 | 0.005 | 3.49E-27 |
| rs9838238 | 3:98600385 | T/C | DCBLD2 | missense | 0.047 | 0.029 | 0.005 | 1.23E-07 | 0.051 | 0.027 | 0.007 | 5.62E-05 | 0.048 | 0.028 | 0.004 | 1.68E-12 |
| rs11722554 | 4:5016883 | G/A | CYTL1 | missense | 0.040 | -0.049 | 0.006 | 2.01E-17 | 0.034 | -0.057 | 0.009 | 6.68E-11 | 0.038 | -0.052 | 0.005 | 1.86E-25 |
| rs61730641 | 4:87730980 | C/T | PTPN13 | missense | 0.015 | -0.086 | 0.010 | 1.94E-19 | 0.016 | -0.094 | 0.012 | 1.38E-15 | 0.016 | -0.089 | 0.008 | 9.43E-32 |
| rs116807401 | 4:135121721 | T/C | PABPC4L | missense | 0.017 | 0.065 | 0.009 | 1.39E-13 | 0.016 | 0.045 | 0.012 | 1.33E-04 | 0.017 | 0.058 | 0.007 | 7.54E-16 |
| rs28925904 | 4:144359490 | C/T | GAB1 | missense | 0.019 | -0.048 | 0.008 | 1.04E-08 | 0.023 | -0.036 | 0.010 | 3.24E-04 | 0.021 | -0.043 | 0.006 | 4.29E-12 |
| rs34343821 | 4:154557616 | C/T | KIAA0922 | missense | 0.011 | 0.059 | 0.011 | 7.75E-08 | 0.015 | 0.056 | 0.012 | 5.75E-06 | 0.013 | 0.058 | 0.008 | 2.18E-12 |
| rs35658696 | 5:102338811 | A/G | PAM | missense | 0.048 | -0.025 | 0.005 | 3.76E-06 | 0.053 | -0.031 | 0.007 | 8.47E-06 | 0.050 | -0.027 | 0.004 | 1.63E-10 |
| rs34821177 | 5:126250812 | C/T | MARCH3 | missense | 0.036 | 0.034 | 0.006 | 4.25E-08 | 0.029 | 0.027 | 0.009 | 2.45E-03 | 0.034 | 0.032 | 0.005 | 1.67E-10 |
| rs62623707 | 5:135288632 | A/G | LECT2 | missense | 0.044 | -0.030 | 0.006 | 1.02E-07 | 0.049 | -0.024 | 0.007 | 4.77E-04 | 0.046 | -0.027 | 0.005 | 1.36E-09 |
| rs34471628 | 5:172196752 | A/G | DUSP1 | missense | 0.036 | 0.048 | 0.006 | 4.00E-14 | 0.042 | 0.036 | 0.007 | 1.26E-06 | 0.039 | 0.043 | 0.005 | 1.93E-20 |
| rs28932177 | 5:176637471 | G/A | NSD1 | missense | 0.028 | 0.063 | 0.007 | 2.38E-17 | 0.027 | 0.065 | 0.009 | 2.62E-12 | 0.028 | 0.064 | 0.006 | 4.27E-30 |
| rs78247455 | 5:176722005 | G/A | NSD] | missense | 0.023 | -0.083 | 0.008 | 1.86E-26 | 0.025 | -0.085 | 0.010 | 8.42E-18 | 0.024 | -0.084 | 0.006 | 2.32E-41 |
| rs7757648 | 6:30851933 | G/A | DDRI | intron | 0.013 | -0.075 | 0.013 | 1.11E-08 | 0.011 | -0.079 | 0.018 | 1.24E-05 | 0.012 | -0.076 | 0.011 | 4.64E-13 |
| rs34427075 | 6:34730395 | C/T | SNRPC | synonymous | 0.014 | -0.117 | 0.010 | 9.21E-33 | 0.016 | -0.139 | 0.012 | 9.59E-31 | 0.015 | -0.126 | 0.008 | 3.45E-60 |
| rs33966734 | 6:41903798 | C/A | CCND3 | stop sained | 0.013 | -0.140 | 0.017 | 5.51E-17 | 0.011 | -0.101 | 0.018 | 3.41E-08 | 0.012 | -0.122 | 0.012 | 1.28E-22 |
| rs17277546 | 7:99489571 | G/A | TRIM4 | 3′UTR | 0.049 | 0.034 | 0.005 | 3.28E-10 | 0.052 | 0.038 | 0.007 | 2.26E-07 | 0.050 | 0.035 | 0.004 | 1.40E-17 |
| rs7636 | 7:100490077 | G/A | ACHE | synonymous | 0.043 | -0.037 | 0.006 | 8.59E-10 | 0.035 | -0.019 | 0.009 | 2.92E-02 | 0.040 | -0.031 | 0.005 | 2.98E-10 |
| rsl7480616 | 7:135123060 | G/C | CNOT4 | missense | 0.028 | 0.060 | 0.007 | 2.31E-17 | 0.030 | 0.054 | 0.009 | 5.04E-10 | 0.029 | 0.058 | 0.005 | 3.90E-26 |
| rs3136797 | 8:42226805 | C/G | POLB | missense | 0.018 | 0.044 | 0.009 | 1.95E-06 | 0.021 | 0.026 | 0.010 | 1.30E-02 | 0.019 | 0.036 | 0.007 | 1.88E-07 |
| rs11575580 | 9:34660864 | C/T | ILURA | missense | 0.016 | -0.064 | 0.009 | 5.20E-13 | 0.020 | -0.030 | 0.011 | 4.42E-03 | 0.018 | -0.050 | 0.007 | 4.01E-13 |
| rs921122 | 9:95063947 | C/T | NOL8 | missense | 0.039 | 0.041 | 0.009 | 2.56E-06 | 0.040 | 0.018 | 0.008 | 3.45E-02 | 0.040 | 0.029 | 0.006 | 3.33E-06 |
| rs41274586 | 10:79580976 | G/A | DLG5 | missense | 0.017 | -0.058 | 0.009 | 2.72E-11 | 0.017 | -0.076 | 0.012 | 5.15E-11 | 0.017 | -0.065 | 0.007 | 7.66E-20 |
| rs41291604 | 10:97919011 | A/G | ZNF518A | missense | 0.040 | 0.031 | 0.006 | 9.94E-08 | 0.040 | 0.022 | 0.008 | 3.05E-03 | 0.040 | 0.028 | 0.005 | 3.91E-09 |
| rs71455793 | 11:65715204 | G/A | TSGAJOIP | missense | 0.039 | -0.058 | 0.006 | 1.82E-21 | 0.046 | -0.072 | 0.007 | 1.41E-23 | 0.042 | -0.064 | 0.005 | 1.52E-43 |
| rs4072796 | 12:7548996 | C/G | CD163L1 | missense | 0.035 | 0.034 | 0.006 | 4.11E-08 | 0.037 | 0.015 | 0.008 | 6.68E-02 | 0.036 | 0.027 | 0.005 | 1.87E-08 |
| rs61743810 | 12:69140339 | G/C | SLC35E3 | missense | 0.022 | -0.047 | 0.008 | 1.13E-09 | 0.023 | -0.036 | 0.010 | 5.UE-04 | 0.022 | -0.043 | 0.006 | 1.29E-11 |
| rs117801489 | 12:104408832 | T/C | GLT8D2 | missense | 0.017 | 0.053 | 0.009 | 8.72E-10 | 0.028 | 0.062 | 0.010 | 5.82E-10 | 0.022 | 0.057 | 0.007 | 1.60E-17 |
| rs2066674 | 13:50842259 | G/A | DLEU1 | intron | 0.044 | 0.073 | 0.006 | 2.33E-37 | 0.041 | 0.084 | 0.008 | 7.02E-25 | 0.043 | 0.077 | 0.005 | 5.66E-57 |
| rsl7880989 | 14:23313633 | G/A | MMP14 | missense | 0.027 | 0.041 | 0.007 | 1.72E-08 | 0.029 | 0.052 | 0.009 | 7.81E-09 | 0.028 | 0.045 | 0.006 | 3.27E-16 |
| rs34354104 | 14:24707479 | G/A | GMPR2 | missense | 0.048 | 0.045 | 0.005 | 3.67E-16 | 0.050 | 0.047 | 0.007 | 1.34E-11 | 0.049 | 0.046 | 0.004 | 2.13E-29 |
| rs117295933 | 14:45403699 | C/A | KLHL28 | missense | 0.016 | -0.045 | 0.009 | 1.55E-06 | 0.025 | -0.036 | 0.010 | 4.13E-04 | 0.020 | -0.041 | 0.007 | 3.05E-09 |
| rs41286548 | 14:70633411 | C/T | SLC8A3 | missense | 0.021 | -0.054 | 0.008 | 2.49E-11 | 0.026 | -0.045 | 0.009 | 2.02E-06 | 0.023 | -0.050 | 0.006 | 2.03E-16 |
| rs28929474 | 14:94844947 | C/T | SERPINA1 | missense | 0.018 | 0.124 | 0.009 | 1.39E-45 | 0.019 | 0.139 | 0.011 | 2.50E-34 | 0.019 | 0.130 | 0.007 | 1.72E-75 |
| rs41286560 | 14:101349454 | G/T | RTL1 | missense | 0.024 | -0.050 | 0.007 | 1.17E-11 | 0.028 | -0.033 | 0.009 | 2.12E-04 | 0.026 | -0.044 | 0.006 | 2.50E-15 |
| rs116858574 | 15:34520687 | T/C | EMC4 | missense | 0.014 | 0.047 | 0.010 | 1.16E-06 | 0.014 | 0.028 | 0.012 | 2.19E-02 | 0.014 | 0.040 | 0.008 | 1.60E-07 |
| rs34815962 | 15:72462255 | C/T | GRAMD2 | missense | 0.019 | 0.073 | 0.009 | 8.72E-17 | 0.023 | 0.074 | 0.010 | 3.66E-13 | 0.021 | 0.073 | 0.007 | 1.28E-27 |
| rs16942341 | 15:89388905 | C/T | AC AN | synonymous | 0.026 | -0.129 | 0.007 | 4.30E-72 | 0.028 | -0.146 | 0.009 | 1.08E-56 | 0.027 | -0.135 | 0.006 | 3.79E-130 |
| rs61733564 | 16:4812705 | A/G | ZNF500 | missense | 0.032 | 0.056 | 0.007 | 8.61E-17 | 0.032 | 0.044 | 0.009 | 2.34E-07 | 0.032 | 0.051 | 0.005 | 2.89E-21 |
| rsl13388806 | 16:24804954 | A/T | TNRC6A | missense | 0.040 | 0.036 | 0.006 | 1.08E-09 | 0.047 | 0.041 | 0.008 | 1.65E-07 | 0.043 | 0.038 | 0.005 | 1.90E-15 |
| rs8052655 | 16:67409180 | G/A | LRRC36 | missense | 0.043 | -0.054 | 0.006 | 1.08E-18 | 0.043 | -0.055 | 0.008 | 3.91E-13 | 0.043 | -0.054 | 0.005 | 6.40E-31 |
| rs77542162 | 17:67081278 | A/G | ABCA6 | missense | 0.017 | 0.049 | 0.010 | 2.17E-06 | 0.023 | 0.051 | 0.010 | 5.58E-07 | 0.020 | 0.050 | 0.007 | 5.57E-12 |
| rs77169818 | 18:74980601 | A/T | GALRl | missense | 0.047 | -0.048 | 0.006 | 3.60E-18 | 0.038 | -0.035 | 0.008 | 3.64E-05 | 0.044 | -0.044 | 0.005 | 5.11E-19 |
| rs3208856 | 19:45296806 | C/T | CBLC | missense | 0.034 | 0.036 | 0.007 | 1.48E-07 | 0.034 | 0.021 | 0.008 | 1.19E-02 | 0.034 | 0.030 | 0.005 | 2.96E-08 |
| rs4252548 | 19:55879672 | C/T | IL11 | missense | 0.026 | -0.114 | 0.007 | 1.02E-57 | 0.022 | -0.101 | 0.010 | 2.28E-23 | 0.025 | -0.110 | 0.006 | 5.32E-81 |
| rs147110934 | 19:55993436 | G/T | ZNF628 | missense | 0.021 | -0.084 | 0.010 | 2.28E-18 | 0.022 | -0.098 | 0.011 | 1.17E-18 | 0.022 | -0.090 | 0.007 | 6.33E-34 |
| rs77885044 | 22:28501414 | C/T | TTC28 | missense | 0.012 | -0.067 | 0.010 | 9.47E-11 | 0.017 | -0.069 | 0.012 | 3.24E-09 | 0.014 | -0.068 | 0.008 | 3.93E-19 |
| rs147348682 | 22:42095658 | T/G | MEII | missense | 0.025 | 0.041 | 0.007 | 2.25E-08 | 0.034 | 0.024 | 0.009 | 6.59E-03 | 0.029 | 0.034 | 0.006 | 3.70E-10 |