TWAS21 significant features
genetically predicted molecular phenotype–trait associations
Trait-Gene Evidence
Evidence Overview
significant and quality-controlled evidence available for the selected trait
Significant GWAS Variants
2,875
P < 2.232e-06
Candidate Genes
70
Unique genes supported by integrated analyses
Evidence Methods
4 / 4
Methods with at least one supported result
Most Supported Gene
LOC_Os03g29350
5 method–layer supports
GWAS Association Signals
genome-wide association landscape for Grain length
Significant GWAS Variants (2875)
showing the top 200 of 2875 variants by P value
| Chr | Position | Variant | P Value | Beta | SE | Effect | Other | AF |
|---|---|---|---|---|---|---|---|---|
| Chr3 | 16,733,441 | chr03:16733441 | 2.782e-21 | 0.522 | 0.0507 | T | G | 0.365 |
| Chr3 | 16,706,516 | chr03:16706516 | 5.879e-21 | 0.501 | 0.0491 | T | C | 0.374 |
| Chr3 | 16,678,042 | chr03:16678042 | 5.342e-20 | 0.483 | 0.0488 | A | C | 0.364 |
| Chr3 | 16,668,900 | chr03:16668900 | 5.192e-18 | 0.458 | 0.0494 | A | T | 0.372 |
| Chr3 | 16,668,465 | chr03:16668465 | 6.189e-18 | 0.457 | 0.0494 | T | C | 0.373 |
| Chr3 | 16,746,075 | chr03:16746075 | 2.146e-17 | -0.461 | 0.0508 | G | A | 0.416 |
| Chr3 | 16,732,850 | chr03:16732850 | 5.344e-17 | -0.476 | 0.0533 | G | A | 0.403 |
| Chr3 | 16,718,368 | chr03:16718368 | 6.298e-17 | -0.466 | 0.0523 | T | G | 0.416 |
| Chr3 | 16,746,080 | chr03:16746080 | 9.566e-17 | -0.456 | 0.0515 | T | G | 0.413 |
| Chr3 | 16,724,778 | chr03:16724778 | 1.362e-16 | -0.484 | 0.0549 | C | T | 0.398 |
| Chr3 | 16,711,171 | chr03:16711171 | 2.182e-16 | -0.459 | 0.0525 | A | G | 0.409 |
| Chr3 | 16,724,772 | chr03:16724772 | 2.981e-16 | -0.48 | 0.0552 | G | T | 0.396 |
| Chr3 | 16,753,112 | chr03:16753112 | 3.103e-16 | -0.449 | 0.0516 | G | A | 0.416 |
| Chr3 | 16,744,754 | chr03:16744754 | 4.141e-16 | -0.447 | 0.0516 | C | T | 0.423 |
| Chr3 | 16,724,816 | chr03:16724816 | 4.790e-16 | -0.474 | 0.0549 | T | C | 0.394 |
| Chr3 | 16,724,355 | chr03:16724355 | 4.856e-16 | -0.476 | 0.0552 | G | A | 0.391 |
| Chr3 | 16,693,989 | chr03:16693989 | 5.351e-16 | -0.455 | 0.0528 | G | A | 0.421 |
| Chr3 | 16,722,620 | chr03:16722620 | 5.491e-16 | -0.462 | 0.0536 | G | T | 0.374 |
| Chr3 | 16,724,810 | chr03:16724810 | 5.530e-16 | -0.476 | 0.0553 | T | A | 0.39 |
| Chr3 | 16,732,896 | chr03:16732896 | 5.801e-16 | -0.468 | 0.0544 | G | T | 0.404 |
| Chr3 | 16,724,730 | chr03:16724730 | 5.905e-16 | -0.473 | 0.055 | G | A | 0.396 |
| Chr3 | 16,724,624 | chr03:16724624 | 6.115e-16 | -0.472 | 0.0549 | G | A | 0.389 |
| Chr3 | 16,757,066 | chr03:16757066 | 7.152e-16 | -0.443 | 0.0517 | T | C | 0.413 |
| Chr3 | 16,713,685 | chr03:16713685 | 7.334e-16 | -0.461 | 0.0538 | G | A | 0.378 |
| Chr3 | 16,748,820 | chr03:16748820 | 8.079e-16 | -0.442 | 0.0517 | C | T | 0.423 |
| Chr3 | 16,749,956 | chr03:16749956 | 8.079e-16 | -0.442 | 0.0517 | G | A | 0.423 |
| Chr3 | 16,716,619 | chr03:16716619 | 9.213e-16 | -0.474 | 0.0555 | A | T | 0.385 |
| Chr3 | 16,732,415 | chr03:16732415 | 9.588e-16 | -0.451 | 0.0529 | T | G | 0.406 |
| Chr3 | 16,693,930 | chr03:16693930 | 1.036e-15 | -0.449 | 0.0527 | G | A | 0.42 |
| Chr3 | 16,718,018 | chr03:16718018 | 1.075e-15 | -0.446 | 0.0524 | G | A | 0.415 |
| Chr3 | 16,734,333 | chr03:16734333 | 1.211e-15 | -0.453 | 0.0533 | A | C | 0.407 |
| Chr3 | 16,725,856 | chr03:16725856 | 1.219e-15 | -0.451 | 0.0532 | C | A | 0.415 |
| Chr3 | 16,724,298 | chr03:16724298 | 1.351e-15 | -0.462 | 0.0544 | T | C | 0.377 |
| Chr3 | 16,724,241 | chr03:16724241 | 1.366e-15 | -0.464 | 0.0548 | C | T | 0.391 |
| Chr3 | 16,718,475 | chr03:16718475 | 1.562e-15 | -0.448 | 0.0529 | T | A | 0.421 |
| Chr3 | 16,718,672 | chr03:16718672 | 1.562e-15 | -0.448 | 0.0529 | G | A | 0.421 |
| Chr3 | 16,718,846 | chr03:16718846 | 1.562e-15 | -0.448 | 0.0529 | C | T | 0.421 |
| Chr3 | 16,686,966 | chr03:16686966 | 1.589e-15 | -0.434 | 0.0513 | AAAG | A | 0.423 |
| Chr3 | 16,746,417 | chr03:16746417 | 1.628e-15 | -0.435 | 0.0515 | T | A | 0.416 |
| Chr3 | 16,724,294 | chr03:16724294 | 1.671e-15 | -0.458 | 0.0543 | T | G | 0.399 |
| Chr3 | 16,728,281 | chr03:16728281 | 1.707e-15 | -0.444 | 0.0526 | G | T | 0.414 |
| Chr3 | 16,757,496 | chr03:16757496 | 1.792e-15 | -0.436 | 0.0517 | TC | T | 0.42 |
| Chr3 | 16,700,676 | chr03:16700676 | 1.916e-15 | -0.443 | 0.0526 | G | A | 0.42 |
| Chr3 | 16,705,883 | chr03:16705883 | 1.916e-15 | -0.443 | 0.0526 | A | G | 0.42 |
| Chr3 | 16,712,650 | chr03:16712650 | 1.916e-15 | -0.443 | 0.0526 | C | T | 0.42 |
| Chr3 | 16,720,151 | chr03:16720151 | 1.928e-15 | -0.465 | 0.0552 | T | C | 0.379 |
| Chr3 | 16,728,308 | chr03:16728308 | 1.928e-15 | -0.465 | 0.0552 | C | T | 0.379 |
| Chr3 | 16,745,689 | chr03:16745689 | 1.988e-15 | -0.434 | 0.0516 | T | C | 0.42 |
| Chr3 | 16,746,791 | chr03:16746791 | 1.988e-15 | -0.434 | 0.0516 | G | A | 0.42 |
| Chr3 | 16,747,072 | chr03:16747072 | 1.988e-15 | -0.434 | 0.0516 | G | A | 0.42 |
| Chr3 | 16,749,678 | chr03:16749678 | 1.988e-15 | -0.434 | 0.0516 | T | C | 0.42 |
| Chr3 | 16,749,801 | chr03:16749801 | 1.988e-15 | -0.434 | 0.0516 | C | T | 0.42 |
| Chr3 | 16,750,033 | chr03:16750033 | 1.988e-15 | -0.434 | 0.0516 | G | A | 0.42 |
| Chr3 | 16,750,497 | chr03:16750497 | 1.988e-15 | -0.434 | 0.0516 | C | CT | 0.42 |
| Chr3 | 16,752,908 | chr03:16752908 | 1.988e-15 | -0.434 | 0.0516 | G | A | 0.42 |
| Chr3 | 16,753,030 | chr03:16753030 | 1.988e-15 | -0.434 | 0.0516 | A | G | 0.42 |
| Chr3 | 16,753,383 | chr03:16753383 | 1.988e-15 | -0.434 | 0.0516 | G | A | 0.42 |
| Chr3 | 16,732,910 | chr03:16732910 | 2.018e-15 | -0.461 | 0.0548 | T | G | 0.406 |
| Chr3 | 16,725,771 | chr03:16725771 | 2.039e-15 | -0.461 | 0.0547 | A | G | 0.375 |
| Chr3 | 16,757,207 | chr03:16757207 | 2.064e-15 | -0.432 | 0.0514 | C | A | 0.416 |
| Chr3 | 16,718,007 | chr03:16718007 | 2.219e-15 | -0.442 | 0.0526 | C | G | 0.411 |
| Chr3 | 16,734,646 | chr03:16734646 | 2.310e-15 | -0.451 | 0.0537 | A | G | 0.413 |
| Chr3 | 16,732,254 | chr03:16732254 | 2.329e-15 | -0.441 | 0.0525 | T | TTTTTG | 0.409 |
| Chr3 | 16,725,235 | chr03:16725235 | 2.365e-15 | -0.461 | 0.0549 | A | G | 0.378 |
| Chr3 | 16,726,768 | chr03:16726768 | 2.365e-15 | -0.461 | 0.0549 | A | G | 0.378 |
| Chr3 | 16,732,936 | chr03:16732936 | 2.374e-15 | -0.456 | 0.0543 | A | G | 0.408 |
| Chr3 | 16,731,043 | chr03:16731043 | 2.704e-15 | -0.444 | 0.053 | C | T | 0.414 |
| Chr3 | 16,732,887 | chr03:16732887 | 2.918e-15 | -0.452 | 0.0541 | G | A | 0.406 |
| Chr3 | 16,709,056 | chr03:16709056 | 2.976e-15 | -0.465 | 0.0556 | C | T | 0.375 |
| Chr3 | 16,719,628 | chr03:16719628 | 3.105e-15 | -0.447 | 0.0535 | C | T | 0.414 |
| Chr3 | 16,733,872 | chr03:16733872 | 3.226e-15 | -0.44 | 0.0527 | G | T | 0.413 |
| Chr3 | 16,698,809 | chr03:16698809 | 3.253e-15 | -0.44 | 0.0526 | G | C | 0.409 |
| Chr3 | 16,744,862 | chr03:16744862 | 3.480e-15 | -0.434 | 0.052 | AG | A | 0.418 |
| Chr3 | 16,745,263 | chr03:16745263 | 3.480e-15 | -0.434 | 0.052 | G | A | 0.418 |
| Chr3 | 16,747,544 | chr03:16747544 | 3.480e-15 | -0.434 | 0.052 | A | G | 0.418 |
| Chr3 | 16,747,580 | chr03:16747580 | 3.480e-15 | -0.434 | 0.052 | G | A | 0.418 |
| Chr3 | 16,748,520 | chr03:16748520 | 3.480e-15 | -0.434 | 0.052 | C | T | 0.418 |
| Chr3 | 16,748,573 | chr03:16748573 | 3.480e-15 | -0.434 | 0.052 | C | T | 0.418 |
| Chr3 | 16,749,802 | chr03:16749802 | 3.480e-15 | -0.434 | 0.052 | G | T | 0.418 |
| Chr3 | 16,724,402 | chr03:16724402 | 3.718e-15 | -0.463 | 0.0556 | G | C | 0.384 |
| Chr3 | 16,732,523 | chr03:16732523 | 3.770e-15 | -0.442 | 0.0531 | C | T | 0.416 |
| Chr3 | 16,732,765 | chr03:16732765 | 3.770e-15 | -0.442 | 0.0531 | G | A | 0.416 |
| Chr3 | 16,732,889 | chr03:16732889 | 3.959e-15 | -0.45 | 0.0541 | C | T | 0.405 |
| Chr3 | 16,717,195 | chr03:16717195 | 4.042e-15 | -0.44 | 0.0528 | G | A | 0.418 |
| Chr3 | 16,725,803 | chr03:16725803 | 4.042e-15 | -0.44 | 0.0528 | G | A | 0.418 |
| Chr3 | 16,725,816 | chr03:16725816 | 4.042e-15 | -0.44 | 0.0528 | C | A | 0.418 |
| Chr3 | 16,726,481 | chr03:16726481 | 4.042e-15 | -0.44 | 0.0528 | G | A | 0.418 |
| Chr3 | 16,726,485 | chr03:16726485 | 4.042e-15 | -0.44 | 0.0528 | G | A | 0.418 |
| Chr3 | 16,727,537 | chr03:16727537 | 4.042e-15 | -0.44 | 0.0528 | G | A | 0.418 |
| Chr3 | 16,728,084 | chr03:16728084 | 4.042e-15 | -0.44 | 0.0528 | C | T | 0.418 |
| Chr3 | 16,728,550 | chr03:16728550 | 4.042e-15 | -0.44 | 0.0528 | T | C | 0.418 |
| Chr3 | 16,728,561 | chr03:16728561 | 4.042e-15 | -0.44 | 0.0528 | C | T | 0.418 |
| Chr3 | 16,754,446 | chr03:16754446 | 4.294e-15 | -0.429 | 0.0516 | TG | T | 0.416 |
| Chr3 | 16,757,322 | chr03:16757322 | 4.294e-15 | -0.429 | 0.0516 | C | T | 0.416 |
| Chr3 | 16,760,651 | chr03:16760651 | 4.294e-15 | -0.429 | 0.0516 | C | T | 0.416 |
| Chr3 | 16,760,746 | chr03:16760746 | 4.294e-15 | -0.429 | 0.0516 | C | T | 0.416 |
| Chr3 | 16,760,803 | chr03:16760803 | 4.294e-15 | -0.429 | 0.0516 | G | A | 0.416 |
| Chr3 | 16,752,277 | chr03:16752277 | 4.368e-15 | -0.433 | 0.0522 | A | G | 0.415 |
| Chr3 | 16,756,492 | chr03:16756492 | 4.368e-15 | -0.433 | 0.0522 | C | T | 0.415 |
| Chr3 | 16,706,508 | chr03:16706508 | 4.399e-15 | -0.433 | 0.0522 | A | G | 0.413 |
| Chr3 | 16,713,654 | chr03:16713654 | 4.399e-15 | -0.433 | 0.0522 | A | C | 0.413 |
| Chr3 | 16,713,671 | chr03:16713671 | 4.399e-15 | -0.433 | 0.0522 | AG | A | 0.413 |
| Chr3 | 16,707,705 | chr03:16707705 | 4.687e-15 | -0.432 | 0.0521 | A | G | 0.413 |
| Chr3 | 16,711,885 | chr03:16711885 | 4.687e-15 | -0.432 | 0.0521 | C | T | 0.413 |
| Chr3 | 16,697,605 | chr03:16697605 | 4.796e-15 | -0.436 | 0.0525 | A | C | 0.416 |
| Chr3 | 16,699,913 | chr03:16699913 | 4.796e-15 | -0.436 | 0.0525 | G | A | 0.416 |
| Chr3 | 16,701,950 | chr03:16701950 | 4.796e-15 | -0.436 | 0.0525 | A | G | 0.416 |
| Chr3 | 16,702,037 | chr03:16702037 | 4.796e-15 | -0.436 | 0.0525 | C | A | 0.416 |
| Chr3 | 16,704,606 | chr03:16704606 | 4.796e-15 | -0.436 | 0.0525 | G | A | 0.416 |
| Chr3 | 16,705,168 | chr03:16705168 | 4.796e-15 | -0.436 | 0.0525 | T | A | 0.416 |
| Chr3 | 16,705,394 | chr03:16705394 | 4.796e-15 | -0.436 | 0.0525 | T | A | 0.416 |
| Chr3 | 16,705,800 | chr03:16705800 | 4.796e-15 | -0.436 | 0.0525 | C | T | 0.416 |
| Chr3 | 16,706,499 | chr03:16706499 | 4.796e-15 | -0.436 | 0.0525 | C | A | 0.416 |
| Chr3 | 16,706,550 | chr03:16706550 | 4.796e-15 | -0.436 | 0.0525 | G | T | 0.416 |
| Chr3 | 16,707,260 | chr03:16707260 | 4.796e-15 | -0.436 | 0.0525 | G | A | 0.416 |
| Chr3 | 16,707,423 | chr03:16707423 | 4.796e-15 | -0.436 | 0.0525 | A | AATC | 0.416 |
| Chr3 | 16,707,611 | chr03:16707611 | 4.796e-15 | -0.436 | 0.0525 | C | T | 0.416 |
| Chr3 | 16,707,653 | chr03:16707653 | 4.796e-15 | -0.436 | 0.0525 | A | C | 0.416 |
| Chr3 | 16,707,716 | chr03:16707716 | 4.796e-15 | -0.436 | 0.0525 | T | C | 0.416 |
| Chr3 | 16,707,862 | chr03:16707862 | 4.796e-15 | -0.436 | 0.0525 | G | A | 0.416 |
| Chr3 | 16,707,897 | chr03:16707897 | 4.796e-15 | -0.436 | 0.0525 | T | A | 0.416 |
| Chr3 | 16,708,131 | chr03:16708131 | 4.796e-15 | -0.436 | 0.0525 | T | C | 0.416 |
| Chr3 | 16,708,948 | chr03:16708948 | 4.796e-15 | -0.436 | 0.0525 | C | T | 0.416 |
| Chr3 | 16,708,968 | chr03:16708968 | 4.796e-15 | -0.436 | 0.0525 | G | A | 0.416 |
| Chr3 | 16,711,541 | chr03:16711541 | 4.796e-15 | -0.436 | 0.0525 | G | A | 0.416 |
| Chr3 | 16,712,810 | chr03:16712810 | 4.796e-15 | -0.436 | 0.0525 | C | A | 0.416 |
| Chr3 | 16,713,093 | chr03:16713093 | 4.796e-15 | -0.436 | 0.0525 | T | C | 0.416 |
| Chr3 | 16,713,226 | chr03:16713226 | 4.796e-15 | -0.436 | 0.0525 | G | A | 0.416 |
| Chr3 | 16,713,302 | chr03:16713302 | 4.796e-15 | -0.436 | 0.0525 | A | C | 0.416 |
| Chr3 | 16,714,782 | chr03:16714782 | 4.796e-15 | -0.436 | 0.0525 | G | A | 0.416 |
| Chr3 | 16,715,120 | chr03:16715120 | 4.796e-15 | -0.436 | 0.0525 | CATT | C | 0.416 |
| Chr3 | 16,726,090 | chr03:16726090 | 4.796e-15 | -0.436 | 0.0525 | A | AT | 0.416 |
| Chr3 | 16,750,064 | chr03:16750064 | 4.814e-15 | -0.428 | 0.0517 | C | T | 0.42 |
| Chr3 | 16,726,145 | chr03:16726145 | 5.125e-15 | -0.437 | 0.0527 | G | A | 0.414 |
| Chr3 | 16,727,679 | chr03:16727679 | 5.125e-15 | -0.437 | 0.0527 | T | C | 0.414 |
| Chr3 | 16,728,485 | chr03:16728485 | 5.367e-15 | -0.463 | 0.056 | G | C | 0.375 |
| Chr3 | 16,719,032 | chr03:16719032 | 5.490e-15 | -0.443 | 0.0536 | T | C | 0.418 |
| Chr3 | 16,727,716 | chr03:16727716 | 5.490e-15 | -0.443 | 0.0536 | T | C | 0.418 |
| Chr3 | 16,707,592 | chr03:16707592 | 5.516e-15 | -0.432 | 0.0523 | G | A | 0.413 |
| Chr3 | 16,714,560 | chr03:16714560 | 5.516e-15 | -0.432 | 0.0523 | T | C | 0.413 |
| Chr3 | 16,716,839 | chr03:16716839 | 5.612e-15 | -0.438 | 0.053 | C | CTTAA | 0.42 |
| Chr3 | 16,718,780 | chr03:16718780 | 5.612e-15 | -0.438 | 0.053 | T | A | 0.42 |
| Chr3 | 16,718,807 | chr03:16718807 | 5.612e-15 | -0.438 | 0.053 | C | T | 0.42 |
| Chr3 | 16,719,193 | chr03:16719193 | 5.612e-15 | -0.438 | 0.053 | C | G | 0.42 |
| Chr3 | 16,719,744 | chr03:16719744 | 5.612e-15 | -0.438 | 0.053 | C | T | 0.42 |
| Chr3 | 16,720,461 | chr03:16720461 | 5.612e-15 | -0.438 | 0.053 | G | GC | 0.42 |
| Chr3 | 16,720,463 | chr03:16720463 | 5.612e-15 | -0.438 | 0.053 | T | A | 0.42 |
| Chr3 | 16,720,666 | chr03:16720666 | 5.612e-15 | -0.438 | 0.053 | G | A | 0.42 |
| Chr3 | 16,720,796 | chr03:16720796 | 5.612e-15 | -0.438 | 0.053 | C | T | 0.42 |
| Chr3 | 16,720,915 | chr03:16720915 | 5.612e-15 | -0.438 | 0.053 | C | T | 0.42 |
| Chr3 | 16,722,539 | chr03:16722539 | 5.612e-15 | -0.438 | 0.053 | G | A | 0.42 |
| Chr3 | 16,725,157 | chr03:16725157 | 5.612e-15 | -0.438 | 0.053 | C | T | 0.42 |
| Chr3 | 16,725,709 | chr03:16725709 | 5.612e-15 | -0.438 | 0.053 | C | T | 0.42 |
| Chr3 | 16,726,427 | chr03:16726427 | 5.612e-15 | -0.438 | 0.053 | T | C | 0.42 |
| Chr3 | 16,726,534 | chr03:16726534 | 5.612e-15 | -0.438 | 0.053 | C | T | 0.42 |
| Chr3 | 16,728,266 | chr03:16728266 | 5.612e-15 | -0.438 | 0.053 | C | T | 0.42 |
| Chr3 | 16,728,961 | chr03:16728961 | 5.612e-15 | -0.438 | 0.053 | G | A | 0.42 |
| Chr3 | 16,716,450 | chr03:16716450 | 5.617e-15 | -0.435 | 0.0526 | T | C | 0.432 |
| Chr3 | 16,710,034 | chr03:16710034 | 5.682e-15 | -0.437 | 0.0529 | G | T | 0.413 |
| Chr3 | 16,721,856 | chr03:16721856 | 5.915e-15 | -0.462 | 0.0559 | A | G | 0.372 |
| Chr3 | 16,752,973 | chr03:16752973 | 6.126e-15 | -0.432 | 0.0524 | A | G | 0.418 |
| Chr3 | 16,728,044 | chr03:16728044 | 6.170e-15 | -0.438 | 0.053 | G | A | 0.415 |
| Chr3 | 16,715,980 | chr03:16715980 | 6.684e-15 | -0.439 | 0.0532 | T | G | 0.416 |
| Chr3 | 16,721,493 | chr03:16721493 | 6.690e-15 | -0.439 | 0.0533 | T | C | 0.415 |
| Chr3 | 16,726,742 | chr03:16726742 | 6.690e-15 | -0.439 | 0.0533 | T | C | 0.415 |
| Chr3 | 16,729,492 | chr03:16729492 | 6.690e-15 | -0.439 | 0.0533 | G | A | 0.415 |
| Chr3 | 16,732,831 | chr03:16732831 | 6.737e-15 | -0.443 | 0.0538 | G | A | 0.405 |
| Chr3 | 16,727,284 | chr03:16727284 | 7.125e-15 | -0.435 | 0.0529 | T | G | 0.416 |
| Chr3 | 16,757,381 | chr03:16757381 | 7.309e-15 | -0.425 | 0.0516 | C | A | 0.411 |
| Chr3 | 16,756,432 | chr03:16756432 | 7.375e-15 | -0.428 | 0.0521 | C | T | 0.414 |
| Chr3 | 16,759,724 | chr03:16759724 | 7.375e-15 | -0.428 | 0.0521 | G | T | 0.414 |
| Chr3 | 16,760,067 | chr03:16760067 | 7.375e-15 | -0.428 | 0.0521 | C | T | 0.414 |
| Chr3 | 16,747,529 | chr03:16747529 | 7.583e-15 | -0.429 | 0.0522 | T | C | 0.416 |
| Chr3 | 16,747,592 | chr03:16747592 | 7.583e-15 | -0.429 | 0.0522 | G | A | 0.416 |
| Chr3 | 16,747,868 | chr03:16747868 | 7.583e-15 | -0.429 | 0.0522 | T | C | 0.416 |
| Chr3 | 16,748,185 | chr03:16748185 | 7.583e-15 | -0.429 | 0.0522 | T | C | 0.416 |
| Chr3 | 16,748,555 | chr03:16748555 | 7.583e-15 | -0.429 | 0.0522 | T | C | 0.416 |
| Chr3 | 16,748,993 | chr03:16748993 | 7.583e-15 | -0.429 | 0.0522 | G | A | 0.416 |
| Chr3 | 16,750,348 | chr03:16750348 | 7.583e-15 | -0.429 | 0.0522 | A | G | 0.416 |
| Chr3 | 16,750,891 | chr03:16750891 | 7.583e-15 | -0.429 | 0.0522 | C | CA | 0.416 |
| Chr3 | 16,753,010 | chr03:16753010 | 7.583e-15 | -0.429 | 0.0522 | T | C | 0.416 |
| Chr3 | 16,719,451 | chr03:16719451 | 7.667e-15 | -0.435 | 0.0529 | A | G | 0.413 |
| Chr3 | 16,722,356 | chr03:16722356 | 7.719e-15 | -0.433 | 0.0527 | G | C | 0.404 |
| Chr3 | 16,722,374 | chr03:16722374 | 7.719e-15 | -0.433 | 0.0527 | C | T | 0.404 |
| Chr3 | 16,752,341 | chr03:16752341 | 7.748e-15 | -0.429 | 0.0522 | C | T | 0.408 |
| Chr3 | 16,705,165 | chr03:16705165 | 7.950e-15 | -0.435 | 0.053 | A | T | 0.414 |
| Chr3 | 16,706,705 | chr03:16706705 | 7.950e-15 | -0.435 | 0.053 | C | CAAA | 0.414 |
| Chr3 | 16,706,803 | chr03:16706803 | 7.950e-15 | -0.435 | 0.053 | G | A | 0.414 |
| Chr3 | 16,726,766 | chr03:16726766 | 7.950e-15 | -0.435 | 0.053 | C | T | 0.414 |
| Chr3 | 16,718,953 | chr03:16718953 | 8.014e-15 | -0.435 | 0.053 | G | T | 0.418 |
| Chr3 | 16,719,752 | chr03:16719752 | 8.069e-15 | -0.438 | 0.0534 | A | T | 0.413 |
| Chr3 | 16,731,141 | chr03:16731141 | 8.424e-15 | -0.439 | 0.0535 | C | G | 0.411 |
| Chr3 | 16,719,056 | chr03:16719056 | 8.981e-15 | -0.437 | 0.0533 | A | G | 0.415 |
| Chr3 | 16,722,012 | chr03:16722012 | 9.241e-15 | -0.432 | 0.0527 | G | T | 0.409 |
| Chr3 | 16,721,431 | chr03:16721431 | 9.244e-15 | -0.438 | 0.0534 | C | T | 0.418 |
| Chr3 | 16,721,739 | chr03:16721739 | 9.244e-15 | -0.438 | 0.0534 | C | T | 0.418 |
| Chr3 | 16,723,068 | chr03:16723068 | 9.244e-15 | -0.438 | 0.0534 | G | A | 0.418 |
| Chr3 | 16,729,325 | chr03:16729325 | 9.244e-15 | -0.438 | 0.0534 | C | T | 0.418 |
| Chr3 | 16,681,312 | chr03:16681312 | 9.257e-15 | -0.433 | 0.0528 | G | C | 0.413 |
| Chr3 | 16,752,315 | chr03:16752315 | 9.314e-15 | -0.429 | 0.0523 | G | C | 0.414 |
Method Details
genetically predicted molecular phenotype–trait associations for Grain length
TWAS Evidence for Grain length
eQTL associations with the Bonferroni threshold shown
Significant TWAS Features (7)
| Gene | Molecular Feature | Locus | TWAS.Z | TWAS.P | Threshold | Model | CV R² | CV P | HSQ | Best GWAS | Best GWAS Z | QTL Variant | QTL R² | QTL Z | QTL·GWAS Z | NSNP | NWGT |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| LOC_Os03g29340 | LOC_Os03g29340 | Chr3:16,692,517–16,698,316 | 6.83 | 8.780e-12 | 2.453e-06 | lasso | 0.53 | 9.100e-49 | 0.329 | chr03:16733441 | 10.3 | chr03:16705835 | 0.522 | -12.4 | -7.59 | 5,228 | 8 |
| LOC_Os03g29350 | LOC_Os03g29350 | Chr3:16,695,922–16,704,617 | 6.41 | 1.470e-10 | 2.453e-06 | enet | 0.37 | 1.100e-30 | 0.204 | chr03:16733441 | 10.3 | chr03:16689153 | 0.355 | -10.6 | -7.58 | 5,294 | 42 |
| LOC_Os03g29460 | LOC_Os03g29460 | Chr3:16,787,178–16,787,968 | 5.8 | 6.510e-09 | 2.453e-06 | enet | 0.073 | 2.000e-06 | 0.0498 | chr03:16733441 | 10.3 | chr03:16718588 | 0.0392 | -5.48 | -4.47 | 5,516 | 11 |
| LOC_Os03g29630 | LOC_Os03g29630 | Chr3:16,888,876–16,892,201 | 5.59 | 2.270e-08 | 2.453e-06 | lasso | 0.1 | 1.300e-08 | 0.128 | chr03:16733441 | 10.3 | chr03:16862291 | 0.0757 | -5.02 | -5.09 | 5,518 | 2 |
| LOC_Os03g29540 | LOC_Os03g29540 | Chr3:16,836,622–16,840,754 | -5.55 | 2.840e-08 | 2.453e-06 | top1 | 0.33 | 1.200e-26 | 0.179 | chr03:16733441 | 10.3 | chr03:16902140 | 0.328 | 10.2 | -5.55 | 5,453 | 1 |
| LOC_Os03g29740 | LOC_Os03g29740 | Chr3:16,941,146–16,943,327 | -5.45 | 4.980e-08 | 2.453e-06 | enet | 0.54 | 3.400e-50 | 0.236 | chr03:16746075 | -9.07 | chr03:16926413 | 0.474 | 12.3 | -5.42 | 5,545 | 39 |
| LOC_Os03g29410 | LOC_Os03g29410 | Chr3:16,749,300–16,754,225 | 5.23 | 1.730e-07 | 2.453e-06 | enet | 0.25 | 3.600e-20 | 0.254 | chr03:16733441 | 10.3 | chr03:16792084 | 0.181 | -8.58 | -5.62 | 5,641 | 26 |