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Table 3 Comparing significant vs. suggestive logistic regression results

From: The genomic signature of trait-associated variants

 

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