Table 2.
Top genes selected by TWAS analysis (BMD and LM)
| Gene | CHR | BEST.GWAS.ID | NSNP | TWAS.Z | TWAS.P | |
|---|---|---|---|---|---|---|
| BMD | IKZF1 | 7 | rs7779747 | 534 | −6.0490 | 1.46E-09 |
| CHKB | 22 | rs761744 | 263 | −3.9353 | 8.31E-07 | |
| MRFAP1 | 4 | rs7660424 | 493 | 4.8190 | 1.44E-06 | |
| MFSD3 | 8 | rs6558318 | 186 | 4.6027 | 4.17E-06 | |
| ZFYVE20 | 3 | rs17040623 | 490 | 4.4536 | 8.44E-06 | |
| C14orf159 | 14 | rs1286341 | 450 | 4.2027 | 2.64E-05 | |
| P2RX1 | 17 | rs17822998 | 463 | 3.9892 | 6.63E-05 | |
| TXNDC12 | 1 | rs6686632 | 194 | 3.9516 | 7.76E-05 | |
| C21orf89 | 21 | rs2838846 | 522 | −3.8387 | 1.24E-04 | |
| RPS3A | 4 | rs7657668 | 264 | 3.7963 | 1.47E-04 | |
| LM | COPS5 | 8 | rs16933079 | 177 | 6.9761 | 3.03E-12 |
| MRPS33 | 7 | rs10488014 | 378 | −6.2056 | 5.45E-10 | |
| ZNF738 | 19 | rs661453 | 288 | −5.7224 | 1.05E-08 | |
| KIAA0319L | 1 | rs6668101 | 215 | 5.2800 | 1.28E-07 | |
| LPL | 8 | rs1569209 | 679 | 5.1003 | 3.39E-07 | |
| LINC00116 | 2 | rs11904760 | 72 | 4.7872 | 1.69E-06 | |
| MGAT1 | 5 | rs3733754 | 350 | −4.7852 | 1.71E-06 | |
| LEPREL1 | 3 | rs6788300 | 652 | −4.6479 | 3.35E-06 | |
| CD2BP2 | 16 | rs7196298 | 191 | −4.4548 | 8.40E-06 | |
| WNT3 | 17 | rs16941702 | 253 | −4.3818 | 1.18E-05 |
The large-scale Genome-Wide Association Study (GWAS) summary data for BMD and LM acquired from a cohort study, including 10,414 participants. The TWAS.P and TWAS.Z values were calculated by the FUSION approach (http://gusevlab.org/projects/fusion/)
TWAS Transcriptome-Wide Association Study, GWAS Genome-Wide Association Study, BMD Bone mineral density, LM Lean mass, TWAS P TWAS P value, TWAS Z TWAS Z-score, HSQ heritability of genes, NSNP number of SNPs in the locus