Project: r01_doug_adams
64 significantly associated models · 21 unique genes
| # | chr | p0 | p1 | # assoc genes | # joint models | best TWAS P | best SNP P | cond SNP P | % var exp | joint genes |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 2 | 144900859 | 146298381 | 1 | 1 | 1.3e-09 | 1.7e-06 | 1.9e-09 | -57 | Rap2b |
| 2 | 2 | 147028669 | 150452756 | 11 | 1 | 2.0e-08 | 2.5e-08 | 1.0e+00 | 100 | Gmps |
| 3 | 2 | 150527756 | 154576513 | 9 | 2 | 9.7e-09 | 2.8e-09 | 1.0e+00 | 100 | Mlf1 Mfsd1 |
p0: physical position of the start of the locus. p1: physical position of the end of the locus. # joint models: number of models selected by step-wise conditional analysis.
| Trait | chisq ratio | # genes+ | # genes++ | % genes++ | corr | corr P | genes |
|---|---|---|---|---|---|---|---|
| EDL weight in grams | 3.4 | 8 | 0 | 0 | -1 | 1.2e-28 | Schip1 Ssr3 Tiparp Shox2 Mlf1 Mfsd1 Kcnab1 NA |
| Average time between licks in bursts | 9.0 | 3 | 0 | 0 | -1 | 5.1e-06 | Schip1 Mfsd1 Rap2b |
| Std. dev. time between licks in bursts | 10.8 | 1 | 0 | 0 | 0 | 1.0e+00 | Rap2b |
| crf_mi_active_responses | 10.2 | 4 | 0 | 0 | -1 | 6.5e-12 | Ssr3 Tiparp Kcnab1 Rap2b |
| tautz: manual_mpc5 | 10.3 | 8 | 1 | 25 | -1 | 5.0e-19 | Schip1 Ssr3 Tiparp Shox2 Gmps Kcnab1 Rap2b NA |
| tautz: manual_spc22 | 9.3 | 6 | 0 | 0 | 1 | 1.2e-08 | Schip1 Ift80 Ssr3 Mfsd1 AABR07011672.1 Rap2b |
| tautz: manual_mpc9 | 11.2 | 1 | 0 | 0 | 0 | 1.0e+00 | Rap2b |
| tautz: manual_mpc19 | 11.2 | 11 | 0 | 0 | -1 | 1.3e-49 | Schip1 Ssr3 Tiparp Shox2 Mlf1 Gfm1 Mfsd1 AABR07011672.1 Kcnab1 Rsrc1 NA |
chisq ratio: Average Chi2 statistic for the selected genes in the secondary trait, divided by the average statistic for all genes in the secondary trait. # genes+: Shared significant genes at Bonferroni correction. # genes++: Shared significant genes at transcriptome-wide significance. % genes++: Number of [++] genes as a percentage of primary trait’s total joint genes. corr: Correlation of effect sizes across the [+] genes.
| tissue | modality | # hits | % hits/tests | avg chisq |
|---|---|---|---|---|
| Adipose | alternative polyA | 0 | 0.000 | 1.31 |
| Adipose | alternative TSS | 0 | 0.000 | 1.27 |
| Adipose | gene expression | 4 | 0.048 | 1.23 |
| Adipose | isoform ratio | 0 | 0.000 | 1.21 |
| Adipose | intron excision ratio | 0 | 0.000 | 1.32 |
| Adipose | mRNA stability | 1 | 0.029 | 1.23 |
| BLA | alternative polyA | 0 | 0.000 | 1.18 |
| BLA | alternative TSS | 0 | 0.000 | 1.26 |
| BLA | gene expression | 2 | 0.033 | 1.22 |
| BLA | isoform ratio | 2 | 0.114 | 1.17 |
| BLA | intron excision ratio | 0 | 0.000 | 1.20 |
| BLA | mRNA stability | 2 | 0.099 | 1.19 |
| Brain | alternative polyA | 0 | 0.000 | 1.25 |
| Brain | alternative TSS | 3 | 0.175 | 1.24 |
| Brain | gene expression | 4 | 0.044 | 1.18 |
| Brain | isoform ratio | 0 | 0.000 | 1.12 |
| Brain | intron excision ratio | 0 | 0.000 | 1.16 |
| Brain | mRNA stability | 2 | 0.046 | 1.18 |
| Eye | alternative polyA | 0 | 0.000 | 1.26 |
| Eye | alternative TSS | 0 | 0.000 | 0.91 |
| Eye | gene expression | 2 | 0.178 | 1.17 |
| Eye | isoform ratio | 0 | 0.000 | 1.20 |
| Eye | intron excision ratio | 1 | 0.163 | 1.27 |
| Eye | mRNA stability | 0 | 0.000 | 1.14 |
| IL | alternative polyA | 0 | 0.000 | 1.28 |
| IL | alternative TSS | 0 | 0.000 | 1.35 |
| IL | gene expression | 2 | 0.055 | 1.20 |
| IL | isoform ratio | 0 | 0.000 | 1.18 |
| IL | intron excision ratio | 0 | 0.000 | 1.11 |
| IL | mRNA stability | 2 | 0.180 | 1.22 |
| LHb | alternative polyA | 0 | 0.000 | 1.35 |
| LHb | alternative TSS | 3 | 0.857 | 1.56 |
| LHb | gene expression | 0 | 0.000 | 1.24 |
| LHb | isoform ratio | 0 | 0.000 | 1.20 |
| LHb | intron excision ratio | 0 | 0.000 | 1.26 |
| LHb | mRNA stability | 2 | 0.193 | 1.26 |
| Liver | alternative polyA | 0 | 0.000 | 1.25 |
| Liver | alternative TSS | 2 | 0.132 | 1.21 |
| Liver | gene expression | 5 | 0.070 | 1.22 |
| Liver | isoform ratio | 1 | 0.042 | 1.22 |
| Liver | intron excision ratio | 0 | 0.000 | 1.12 |
| Liver | mRNA stability | 1 | 0.041 | 1.21 |
| NAcc | alternative polyA | 0 | 0.000 | 1.21 |
| NAcc | alternative TSS | 0 | 0.000 | 1.40 |
| NAcc | gene expression | 0 | 0.000 | 1.25 |
| NAcc | isoform ratio | 0 | 0.000 | 1.12 |
| NAcc | intron excision ratio | 0 | 0.000 | 1.13 |
| NAcc | mRNA stability | 0 | 0.000 | 1.18 |
| NAcc2 | alternative polyA | 0 | 0.000 | 1.25 |
| NAcc2 | alternative TSS | 0 | 0.000 | 1.25 |
| NAcc2 | gene expression | 2 | 0.037 | 1.20 |
| NAcc2 | isoform ratio | 3 | 0.195 | 1.23 |
| NAcc2 | intron excision ratio | 0 | 0.000 | 1.21 |
| NAcc2 | mRNA stability | 0 | 0.000 | 1.25 |
| OFC | alternative polyA | 0 | 0.000 | 1.23 |
| OFC | alternative TSS | 2 | 0.627 | 1.39 |
| OFC | gene expression | 3 | 0.081 | 1.24 |
| OFC | isoform ratio | 2 | 0.245 | 1.29 |
| OFC | intron excision ratio | 0 | 0.000 | 1.35 |
| OFC | mRNA stability | 1 | 0.093 | 1.20 |
| PL | alternative polyA | 0 | 0.000 | 1.14 |
| PL | alternative TSS | 0 | 0.000 | 1.31 |
| PL | gene expression | 4 | 0.108 | 1.28 |
| PL | isoform ratio | 0 | 0.000 | 1.11 |
| PL | intron excision ratio | 0 | 0.000 | 1.17 |
| PL | mRNA stability | 1 | 0.087 | 1.29 |
| PL2 | alternative polyA | 0 | 0.000 | 1.18 |
| PL2 | alternative TSS | 0 | 0.000 | 1.20 |
| PL2 | gene expression | 3 | 0.047 | 1.22 |
| PL2 | isoform ratio | 0 | 0.000 | 1.08 |
| PL2 | intron excision ratio | 0 | 0.000 | 1.16 |
| PL2 | mRNA stability | 2 | 0.082 | 1.20 |
avg chisq: Average Chi2 (squared Z-score) across all models in this panel for this trait.