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

Kindt et al.

Kindt et al. BMC Genomics 2013 14:108   doi:10.1186/1471-2164-14-108

Open Data