Table 3.
Comparing significant vs. suggestive logistic regression results
| |
Significantly associated SNPs |
Suggestively associated SNPs |
||||||
|---|---|---|---|---|---|---|---|---|
| Annotation | Estimated effect | Std. error | β-coefficient | P-value | Estimated effect | Std. error | β-coefficient | P-value |
| Open Chromatin |
0.79 |
0.06 |
13.31 |
2.00 × 10-40 |
0.15 |
0.04 |
3.43 |
5.94 × 10-04 |
| eQTLs |
0.72 |
0.07 |
10.7 |
1.01 × 10-26 |
0.39 |
0.08 |
5.06 |
4.10 × 10-07 |
| DNase Clusters |
0.46 |
0.05 |
8.52 |
1.58 × 10-17 |
NA |
NA |
NA |
NA |
| Heterochrom; low signal |
−0.37 |
0.05 |
−6.69 |
2.26 × 10-11 |
NA |
NA |
NA |
NA |
| Exons |
0.58 |
0.09 |
6.52 |
6.94 × 10-11 |
0.17 |
0.07 |
2.35 |
1.85 × 10-02 |
| Strong enhancer (A) |
0.47 |
0.08 |
5.98 |
2.29 × 10-09 |
0.21 |
0.1 |
2.12 |
3.37 × 10-02 |
| Transcriptional elongation |
−0.43 |
0.07 |
−5.87 |
4.26 × 10-09 |
NA |
NA |
NA |
NA |
| TSS 5 kb upstream |
0.36 |
0.07 |
5.53 |
3.26 × 10-08 |
NA |
NA |
NA |
NA |
| vega Genes |
0.27 |
0.05 |
5.51 |
3.59 × 10-08 |
0.09 |
0.04 |
2.17 |
2.98 × 10-02 |
| Polycomb repressed |
0.24 |
0.07 |
3.6 |
3.19 × 10-04 |
0.13 |
0.07 |
1.86 |
6.32 × 10-02 |
| Gained Stops |
1.15 |
0.35 |
3.32 |
8.95 × 10-04 |
1.49 |
0.42 |
3.58 |
3.44 × 10-04 |
| Syn. SNPs |
−0.32 |
0.1 |
−3.12 |
1.83 × 10-03 |
NA |
NA |
NA |
NA |
| Non-Syn. SNPs |
0.23 |
0.09 |
2.56 |
1.06 × 10-02 |
NA |
NA |
NA |
NA |
| Active promoter |
−0.25 |
0.1 |
−2.47 |
1.37 × 10-02 |
NA |
NA |
NA |
NA |
| MCS44wayPrimates |
0.17 |
0.07 |
2.33 |
2.00 × 10-02 |
NA |
NA |
NA |
NA |
| MCS44way |
0.24 |
0.11 |
2.31 |
2.07 × 10-02 |
NA |
NA |
NA |
NA |
| 5UTR |
−0.31 |
0.16 |
−2.01 |
4.50 × 10-02 |
NA |
NA |
NA |
NA |
| Inactive/poised promoter |
0.37 |
0.2 |
1.87 |
6.14 × 10-02 |
−0.59 |
0.41 |
−1.43 |
1.54 × 10-01 |
| MCS44wayPlacental |
−0.2 |
0.11 |
−1.8 |
7.14 × 10-02 |
NA |
NA |
NA |
NA |
| Enhancers |
0.53 |
0.29 |
1.8 |
7.22 × 10-02 |
NA |
NA |
NA |
NA |
| Insulator |
−0.18 |
0.1 |
−1.8 |
7.24 × 10-02 |
NA |
NA |
NA |
NA |
| InDels |
0.11 |
0.06 |
1.76 |
7.79 × 10-02 |
NA |
NA |
NA |
NA |
| tSmiRNA |
0.83 |
0.51 |
1.61 |
1.08 × 10-01 |
−9.42 |
66.4 |
−0.14 |
8.87 × 10-01 |
| Weak/poised enhancer (B) |
0.1 |
0.06 |
1.52 |
1.28 × 10-01 |
NA |
NA |
NA |
NA |
| Repetitive/CNV (B) |
−1.41 |
1 |
−1.41 |
1.58 × 10-01 |
NA |
NA |
NA |
NA |
| Repetitive/CNV (A) |
NA |
NA |
NA |
NA |
−0.9 |
0.71 |
−1.27 |
2.05 × 10-01 |
| RNA Genes | NA | NA | NA | NA | −0.73 | 0.58 | −1.26 | 2.08 × 10-01 |