Table 1.
Summary of 87 multiple associated SNPs at 36 loci for height with P < 5 × 10–8 in the joint analysis using the ARIC cohort as a reference sample for LD
| Location (bp) | Nearest gene | GIANT single-SNP meta-analysis |
Joint analysis, LD from ARIC cohort |
||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| SNP | Chr. | Allele 1 | Freq. | β | P | Freq. | b | P | r | q2 (%) | |||
| rs17346452 | 1 | 170319910 | DNM3 | T | 0.727 | –0.038 | 2.5 × 10–19 | 0.059 | 0.706 | –0.040 | 2.8 × 10–21 | 0.109 | 0.062 |
| rs2421992 | 1 | 170507874 | DNM3 | T | 0.701 | 0.021 | 2.6 × 10–6 | 0.713 | 0.025 | 2.6 × 10–8 | 0.023 | ||
| rs6684205 | 1 | 216676325 | TGFB2 | A | 0.714 | –0.033 | 1.6 × 10–15 | 0.045 | 0.711 | –0.035 | 1.9 × 10–17 | 0.051 | 0.048 |
| rs11118171 | 1 | 217114492 | LYPLAL1 | A | 0.631 | 0.025 | 2.2 × 10–10 | 0.644 | 0.025 | 2.4 × 10–10 | –0.084 | 0.030 | |
| rs11118346 | 1 | 217810342 | SLC30A10 | T | 0.464 | –0.026 | 1.7 × 10–12 | 0.036 | 0.469 | –0.025 | 6.9 × 10–12 | 0.035 | |
| rs4665736 | 2 | 25041103 | RBJ | T | 0.535 | 0.034 | 1.3 × 10–18 | 0.058 | 0.533 | 0.029 | 3.7 × 10–14 | 0.123 | 0.050 |
| rs11694842 | 2 | 25336474 | DNMT3A | A | 0.669 | 0.028 | 2.6 × 10–12 | 0.660 | 0.026 | 1.1 × 10–10 | 0.033 | ||
| rs1367226 | 2 | 55943044 | EFEMP1 | A | 0.434 | –0.005 | 2.0 × 10–1 | 0.428 | –0.027 | 5.0 × 10–11 | –0.421 | 0.007 | |
| rs3791675 | 2 | 55964813 | EFEMP1 | T | 0.234 | –0.050 | 1.1 × 10–28 | 0.091 | 0.249 | –0.063 | 3.0 × 10–37 | 0.116 | |
| rs1541777 | 2 | 219295535 | TTLL4 | A | 0.526 | 0.025 | 1.0 × 10–11 | 0.513 | 0.022 | 6.4 × 10–9 | 0.062 | 0.028 | |
| rs6741325 | 2 | 219615943 | CCDC108 | C | 0.902 | 0.048 | 2.0 × 10–14 | 0.043 | 0.902 | 0.044 | 5.2 × 10–12 | 0.060 | 0.039 |
| rs16859517 | 2 | 219657428 | NHEJ1 | T | 0.036 | 0.073 | 5.8 × 10–12 | 0.038 | 0.064 | 2.6 × 10–9 | 0.034 | ||
| rs7598759 | 2 | 232030200 | NCL | T | 0.454 | –0.022 | 6.2 × 10–8 | 0.419 | –0.023 | 1.2 × 10–8 | –0.013 | 0.025 | |
| rs2580816 | 2 | 232506210 | NPPC | T | 0.197 | –0.041 | 7.3 × 10–17 | 0.055 | 0.185 | –0.041 | 2.7 × 10–17 | –0.016 | 0.056 |
| rs7571716 | 2 | 233149664 | EIF4E2 | T | 0.292 | 0.028 | 7.1 × 10–12 | 0.287 | 0.027 | 3.6 × 10–11 | 0.033 | ||
| rs4676386 | 2 | 241423659 | KIF1A | A | 0.483 | 0.023 | 1.5 × 10–9 | 0.477 | 0.022 | 5.7 × 10–9 | –0.028 | 0.027 | |
| rs12694997 | 2 | 241911659 | 37500 | A | 0.244 | –0.027 | 5.4 × 10–10 | 0.029 | 0.234 | –0.027 | 6.2 × 10–10 | 0.028 | |
| rs7652177 | 3 | 173451771 | FNDC3B | C | 0.496 | –0.031 | 3.9 × 10–16 | 0.491 | –0.029 | 1.2 × 10–14 | –0.060 | 0.045 | |
| rs572169 | 3 | 173648421 | GHSR | T | 0.313 | 0.036 | 1.0 × 10–18 | 0.056 | 0.315 | 0.034 | 4.8 × 10–17 | 0.053 | |
| rs6784185 | 3 | 186955759 | IGF2BP2 | A | 0.203 | –0.008 | 8.8 × 10–2 | 0.205 | –0.034 | 2.2 × 10–10 | 0.523 | 0.009 | |
| rs720390 | 3 | 187031377 | IGF2BP2 | A | 0.386 | 0.031 | 1.8 × 10–14 | 0.046 | 0.378 | 0.045 | 1.5 × 10–22 | 0.067 | |
| rs16896276 | 4 | 17624254 | LCORL | A | 0.269 | 0.041 | 8.2 × 10–23 | 0.256 | 0.030 | 1.8 × 10–12 | 0.248 | 0.051 | |
| rs2061455 | 4 | 17644348 | LCORL | A | 0.847 | 0.072 | 7.8 × 10–39 | 0.139 | 0.841 | 0.063 | 7.2 × 10–29 | 0.122 | |
| rs17720281 | 4 | 145763226 | HHIP | T | 0.406 | 0.047 | 1.7 × 10–30 | 0.437 | 0.031 | 9.2 × 10–13 | –0.389 | 0.074 | |
| rs7689420 | 4 | 145787802 | HHIP | T | 0.163 | –0.069 | 1.1 × 10–41 | 0.133 | 0.164 | –0.054 | 2.9 × 10–23 | 0.106 | |
| rs7731703 | 5 | 32730699 | NPR3 | T | 0.312 | –0.030 | 1.4 × 10–10 | 0.324 | –0.032 | 1.4 × 10–11 | –0.143 | 0.043 | |
| rs1173735 | 5 | 32807136 | NPR3 | A | 0.739 | –0.030 | 1.3 × 10–12 | 0.738 | –0.042 | 5.1 × 10–23 | 0.181 | 0.051 | |
| rs1173727 | 5 | 32866278 | C5orf23 | T | 0.394 | 0.036 | 1.5 × 10–20 | 0.063 | 0.409 | 0.040 | 1.4 × 10–24 | –0.071 | 0.070 |
| rs11745439 | 5 | 33265791 | TARS | A | 0.288 | –0.028 | 1.3 × 10–11 | 0.271 | –0.026 | 9.9 × 10–10 | 0.031 | ||
| rs4620037 | 5 | 170807702 | FGF18 | A | 0.801 | 0.032 | 3.6 × 10–12 | 0.788 | 0.035 | 4.2 × 10–14 | 0.049 | 0.037 | |
| rs1529701 | 5 | 170933582 | FGF18 | T | 0.292 | –0.023 | 4.9 × 10–8 | 0.309 | –0.024 | 1.6 × 10–8 | 0.001 | 0.023 | |
| rs12153391 | 5 | 171136043 | FBXW11 | A | 0.255 | –0.033 | 2.4 × 10–13 | 0.042 | 0.244 | –0.033 | 4.3 × 10–13 | 0.027 | 0.042 |
| rs4868126 | 5 | 171216074 | FBXW11 | T | 0.396 | –0.031 | 3.3 × 10–13 | 0.397 | –0.030 | 6.8 × 10–13 | 0.046 | ||
| rs4246079 | 6 | 6834817 | RREB1 | A | 0.118 | –0.039 | 1.9 × 10–9 | 0.124 | –0.039 | 2.5 × 10–9 | 0.001 | 0.033 | |
| rs3812163 | 6 | 7670759 | BMP6 | A | 0.540 | –0.037 | 5.3 × 10–22 | 0.069 | 0.541 | –0.037 | 1.7 × 10–22 | 0.023 | 0.070 |
| rs9942510 | 6 | 7745305 | BMP6 | A | 0.162 | 0.029 | 1.3 × 10–8 | 0.156 | 0.030 | 4.3 × 10–9 | 0.024 | ||
| rs12204421 | 6 | 33736841 | ITPR3 | A | 0.738 | 0.030 | 5.6 × 10–12 | 0.747 | 0.030 | 1.0 × 10–11 | 0.001 | 0.036 | |
| rs12214804 | 6 | 34296844 | HMGA1 | T | 0.925 | –0.079 | 3.5 × 10–26 | 0.090 | 0.922 | –0.082 | 9.9 × 10–28 | 0.064 | 0.093 |
| rs3800461 | 6 | 34724300 | C6orf106 | C | 0.124 | 0.045 | 6.4 × 10–15 | 0.126 | 0.046 | 7.3 × 10–16 | –0.054 | 0.046 | |
| rs6899744 | 6 | 35394273 | DEF6 | T | 0.016 | –0.138 | 2.2 × 10–15 | 0.063 | 0.018 | –0.131 | 5.5 × 10–14 | 0.060 | |
| rs648831 | 6 | 81012927 | BCKDHB | T | 0.493 | 0.028 | 2.7 × 10–13 | 0.509 | 0.025 | 3.5 × 10–11 | –0.064 | 0.036 | |
| rs310402 | 6 | 81857211 | FAM46A | T | 0.462 | –0.030 | 2.6 × 10–15 | 0.045 | 0.452 | –0.028 | 5.6 × 10–14 | 0.042 | |
| rs6569648 | 6 | 130390812 | L3MBTL3 | T | 0.761 | –0.036 | 3.7 × 10–16 | 0.048 | 0.768 | –0.036 | 2.4 × 10–16 | –0.011 | 0.049 |
| rs6921207 | 6 | 131369649 | EPB41L2 | A | 0.366 | 0.021 | 3.0 × 10–8 | 0.362 | 0.021 | 4.9 × 10–8 | 0.022 | ||
| rs543650 | 6 | 152152636 | ESR1 | T | 0.396 | –0.032 | 6.4 × 10–13 | 0.050 | 0.399 | –0.029 | 3.5 × 10–11 | –0.115 | 0.046 |
| rs3020418 | 6 | 152386855 | ESR1 | A | 0.300 | 0.028 | 5.9 × 10–12 | 0.286 | 0.026 | 1.7 × 10–10 | 0.032 | ||
| rs4470914 | 7 | 19583047 | TWISTNB | T | 0.181 | 0.033 | 6.7 × 10–11 | 0.033 | 0.180 | 0.033 | 2.3 × 10–11 | 0.010 | 0.034 |
| rs12538581 | 7 | 20365642 | ITGB8 | A | 0.502 | –0.024 | 4.7 × 10–10 | 0.497 | –0.024 | 1.5 × 10–10 | 0.030 | ||
| rs10958476 | 8 | 57258362 | PLAG1 | T | 0.787 | –0.042 | 1.4 × 10–18 | 0.833 | –0.036 | 1.6 × 10–13 | –0.167 | 0.053 | |
| rs7460090 | 8 | 57356717 | RDHE2 | T | 0.873 | 0.055 | 8.6 × 10–22 | 0.068 | 0.882 | 0.047 | 2.2 × 10–16 | 0.059 | |
| rs473902 | 9 | 97296056 | PTCH1 | T | 0.922 | 0.074 | 7.0 × 10–20 | 0.082 | 0.913 | 0.064 | 7.3 × 10–15 | –0.208 | 0.071 |
| rs10512248 | 9 | 97299524 | PTCH1 | T | 0.660 | –0.033 | 1.5 × 10–16 | 0.658 | –0.026 | 1.2 × 10–10 | –0.020 | 0.040 | |
| rs10990303 | 9 | 97450226 | PTCH1 | T | 0.227 | 0.030 | 1.4 × 10–10 | 0.208 | 0.029 | 2.4 × 10–10 | 0.033 | 0.031 | |
| rs2025151 | 9 | 98201333 | ZNF367 | C | 0.810 | –0.041 | 3.1 × 10–16 | 0.806 | –0.041 | 5.0 × 10–16 | 0.053 | ||
| rs13302480 | 9 | 117505134 | 37226 | C | 0.115 | –0.036 | 7.2 × 10–9 | 0.109 | –0.037 | 1.9 × 10–9 | 0.041 | 0.028 | |
| rs7869550 | 9 | 118174617 | PAPPA | A | 0.796 | 0.030 | 1.5 × 10–10 | 0.029 | 0.799 | 0.031 | 1.6 × 10–11 | 0.031 | |
| rs7849585 | 9 | 138251691 | QSOX2 | T | 0.334 | 0.032 | 4.6 × 10–15 | 0.048 | 0.318 | 0.031 | 3.7 × 10–14 | –0.031 | 0.046 |
| rs8413 | 9 | 138443132 | INPP5E | T | 0.599 | –0.026 | 3.0 × 10–11 | 0.584 | –0.024 | 4.2 × 10–10 | 0.031 | ||
| rs77993 | 10 | 8058852 | ZMIZ1 | A | 0.439 | –0.023 | 2.1 × 10–9 | 0.426 | –0.024 | 3.6 × 10–10 | –0.037 | 0.028 | |
| rs2145998 | 10 | 80791702 | PPIF | A | 0.480 | –0.025 | 2.0 × 10–11 | 0.033 | 0.490 | –0.026 | 7.2 × 10–12 | 0.034 | |
| rs11107116 | 12 | 92502635 | SOCS2 | T | 0.223 | 0.052 | 4.0 × 10–32 | 0.098 | 0.216 | 0.056 | 4.2 × 10–37 | 0.095 | 0.106 |
| rs2885691 | 12 | 92646350 | CRADD | T | 0.436 | –0.029 | 2.3 × 10–14 | 0.439 | –0.034 | 1.1 × 10–18 | 0.049 | ||
| rs7980687 | 12 | 122388664 | SBNO1 | A | 0.206 | 0.036 | 6.7 × 10–14 | 0.043 | 0.192 | 0.034 | 4.0 × 10–13 | 0.045 | 0.041 |
| rs1809889 | 12 | 123367179 | FAM101A | T | 0.290 | 0.032 | 1.1 × 10–12 | 0.293 | 0.030 | 7.7 × 10–12 | 0.040 | ||
| rs12440667 | 15 | 72018492 | LOXL1 | T | 0.467 | –0.028 | 1.4 × 10–12 | 0.481 | –0.030 | 2.2 × 10–14 | –0.051 | 0.043 | |
| rs5742915 | 15 | 72123686 | PML | T | 0.527 | –0.031 | 8.2 × 10–14 | 0.049 | 0.516 | –0.032 | 3.4 × 10–15 | 0.051 | |
| rs11259936 | 15 | 82371586 | ADAMTSL3 | A | 0.484 | –0.042 | 1.4 × 10–29 | 0.091 | 0.484 | –0.038 | 7.5 × 10–24 | –0.164 | 0.082 |
| rs12148239 | 15 | 82432022 | ADAMTSL3 | T | 0.728 | 0.031 | 1.1 × 10–13 | 0.724 | 0.024 | 8.8 × 10–9 | 0.031 | ||
| rs4932429 | 15 | 87164536 | ACAN | C | 0.510 | –0.025 | 2.7 × 10–10 | 0.520 | –0.022 | 2.3 × 10–8 | 0.047 | 0.028 | |
| rs16942341 | 15 | 87189909 | ACAN | T | 0.031 | –0.134 | 2.2 × 10–24 | 0.110 | 0.027 | –0.116 | 1.8 × 10–18 | –0.122 | 0.095 |
| rs2280470* | 15 | 87196630 | ACAN | A | 0.334 | 0.039 | 1.5 × 10–22 | 0.330 | 0.036 | 6.3 × 10–19 | 0.065 | ||
| rs12916269 | 15 | 98347739 | ADAMTS17 | A | 0.426 | –0.028 | 9.8 × 10–13 | 0.409 | –0.030 | 9.6 × 10–15 | –0.069 | 0.043 | |
| rs2035344 | 15 | 98507671 | ADAMTS17 | A | 0.687 | –0.024 | 1.6 × 10–8 | 0.699 | –0.024 | 1.9 × 10–8 | 0.049 | 0.025 | |
| rs4965598 | 15 | 98577137 | ADAMTS17 | T | 0.681 | –0.035 | 1.4 × 10–18 | 0.056 | 0.680 | –0.035 | 1.9 × 10–18 | 0.056 | |
| rs8182364 | 17 | 44373024 | SNF8 | A | 0.461 | 0.023 | 7.8 × 10–10 | 0.462 | 0.021 | 6.8 × 10–9 | 0.044 | 0.025 | |
| rs2072153 | 17 | 44745013 | ZNF652 | C | 0.306 | 0.026 | 7.4 × 10–11 | 0.031 | 0.308 | 0.026 | 4.6 × 10–10 | 0.030 | |
| rs227724 | 17 | 52133816 | C17orf67 | A | 0.657 | –0.027 | 7.0 × 10–12 | 0.035 | 0.656 | –0.026 | 6.9 × 10–11 | –0.029 | 0.033 |
| rs4794665 | 17 | 52205328 | C17orf67 | A | 0.485 | 0.024 | 2.0 × 10–10 | 0.490 | 0.023 | 7.5 × 10–10 | 0.028 | ||
| rs2079795 | 17 | 56851431 | C17orf82 | T | 0.329 | 0.040 | 4.0 × 10–23 | 0.071 | 0.331 | 0.039 | 6.4 × 10–23 | –0.005 | 0.071 |
| rs12451513 | 17 | 56997110 | NACA2 | T | 0.602 | –0.022 | 2.0 × 10–7 | 0.605 | –0.022 | 4.2 × 10–8 | 0.024 | ||
| rs2137143 | 17 | 59159133 | LYK5 | T | 0.055 | 0.049 | 3.1 × 10–8 | 0.059 | 0.062 | 2.8 × 10–12 | 0.147 | 0.033 | |
| rs2727300 | 17 | 59319130 | GH2 | A | 0.275 | 0.037 | 4.1 × 10–18 | 0.056 | 0.281 | 0.041 | 4.7 × 10–22 | 0.062 | |
| rs12458127 | 18 | 44911356 | DYM | T | 0.076 | –0.056 | 1.4 × 10–13 | 0.055 | –0.042 | 3.9 × 10–8 | 0.218 | 0.034 | |
| rs9967417 | 18 | 45213498 | DYM | C | 0.565 | –0.038 | 1.4 × 10–22 | 0.074 | 0.563 | –0.033 | 5.2 × 10–17 | 0.065 | |
| rs6060154 | 20 | 33063262 | TRPC4AP | A | 0.264 | 0.023 | 5.9 × 10–8 | 0.278 | 0.033 | 9.5 × 10–15 | 0.040 | 0.030 | |
| rs143384 | 20 | 33489170 | GDF5 | A | 0.581 | –0.064 | 2.5 × 10–55 | 0.206 | 0.595 | –0.053 | 4.5 × 10–33 | –0.390 | 0.171 |
| rs6060739 | 20 | 34031006 | C20orf152 | T | 0.188 | 0.052 | 2.8 × 10–25 | 0.184 | 0.032 | 2.4 × 10–9 | 0.053 | ||
| Total | 2.5 | 4.1 | |||||||||||
SNPs on different chromosomes or more than 10 Mb distant from each other are assumed to be uncorrelated. The empirical variance of phenotypes of height estimated from the summary statistic is 0.967. Chr., chromosome; allele 1, reference allele; freq.: frequency of the reference allele; β, marginal effect; qL2, variance explained based on marginal SNP effect for the leading SNPs; b, joint effect; q2, variance explained based on the joint SNP effect; r, LD correlation between a SNP and the next adjacent SNP at a locus.