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Table 4 Results from logistic regression analysis

From: Regulatory and coding genome regions are enriched for trait associated variants in dairy and beef cattle

Traits

Intergenic

Upstream

Downstream

Intragenic

Intron

CDS

Synonymous

Missense

UTR (5'&3')

Non-coding conserved

TFBS

micro RNA target

Fat

0.05 (−0.01)

4.92 (0.15)

3.36 (0.12)

0.55 (0.10)

0.17 (−0.11)

4.70 (0.12)

0.00 (0.02)

0.26 (0.10)

0.27 (−0.21)

0.07 (0.02)

0.22 (0.18)

0.55 (−0.16)

Fat Percent

0.68 (−0.08)

6.44 (0.14)

4.89 (0.11)

12.71 (0.52)

0.89 (−0.46)

11.69 (−0.44)

0.29 (0.36)

0.06 (0.38)

0.67 (−0.40)

0.48 (−0.08)

0.26 (−0.32)

1.53 (0.28)

Milk

0.67 (−0.06)

1.91 (0.03)

2.80 (0.05)

2.16 (0.64)

2.12 (−0.66)

3.28 (0.14)

0.84 (−0.66)

0.37 (−0.54)

0.05 (−0.66)

0.93 (−0.10)

0.09 (−0.09)

1.26 (0.20)

Protein

3.05 (−0.17)

2.60 (0.00)

5.12 (0.01)

4.20 (0.39)

1.41 (−0.49)

2.85 (0.06)

0.51 (−0.47)

0.86 (−0.28)

0.19 (−0.46)

1.11 (−0.11)

0.20 (0.13)

0.48 (0.10)

Protein Percent

0.21 (−0.02)

15.12 (0.21)

9.59 (0.17)

5.10 (0.38)

0.84 (−0.33)

8.60 (−0.10)

0.00 (0.00)

0.46 (0.11)

4.06 (−0.06)

0.57 (−0.07)

0.55 (0.29)

0.84 (0.15)

Angularity

0.89 (−0.25)

2.59 (0.11)

1.31 (0.02)

7.74 (−0.75)

0.78 (0.79)

1.41 (0.86)

0.06 (−0.26)

1.12 (0.37)

0.16 (0.38)

0.93 (0.29)

0.09 (0.21)

0.71 (0.40)

BCS

1.14 (−0.60)

2.16 (0.02)

2.12 (0.02)

0.12 (0.34)

0.24 (−0.88)

3.04 (2.44)

2.18 (−3.07)

0.21 (−2.13)

0.00 (−0.81)

0.73 (−0.94)

1.05 (1.66)

0.14 (0.22)

Mammary System

1.27 (0.31)

2.70 (0.51)

1.16 (0.38)

2.54 (1.01)

0.52 (−0.86)

1.51 (−0.45)

0.00 (0.07)

0.04 (0.04)

1.34 (−0.32)

0.64 (−0.31)

0.24 (−5.29)

1.61 (0.65)

Fertility

2.52 (0.90)

1.46 (0.97)

0.15 (0.59)

2.44 (3.86)

5.45 (−3.37)

0.57 (−2.92)

0.16 (0.31)

0.62 (−0.98)

0.04 (−3.33)

0.27 (0.23)

0.17 (−3.91)

0.67 (−3.93)

Survival Direct

4.19 (0.28)

7.40 (0.41)

6.19 (0.39)

3.21 (0.43)

0.32 (−0.23)

0.75 (−0.71)

0.41 (0.62)

0.11 (0.55)

4.97 (0.22)

0.95 (−0.16)

0.13 (0.14)

0.53 (−0.20)

SCC

0.88 (0.30)

0.04 (0.17)

0.82 (0.37)

0.55 (0.06)

0.06 (0.16)

0.05 (0.09)

0.00 (0.00)

0.06 (0.10)

0.72 (0.55)

2.05 (0.51)

0.23 (−5.00)

0.66 (−0.88)

LLPF

0.51 (0.12)

28.17 (0.88)

16.27 (0.74)

10.89 (0.37)

0.06 (0.11)

3.11 (0.22)

0.05 (0.22)

0.40 (−0.08)

1.66 (0.19)

0.99 (−0.43)

0.07 (0.14)

1.50 (0.59)

CIMF

0.00 (0.01)

3.38 (0.46)

0.1 (−0.05)

8.15 (−0.19)

0.32 (0.57)

0.71 (0.55)

0.00 (0.08)

0.04 (0.03)

0.08 (0.35)

0.1 (−0.10)

2.96 (1.87)

0.31 (0.30)

CRIB

0.18 (−0.1)

1.16 (0.21)

0.07 (−0.13)

0.19 (0.06)

0.04 (−0.13)

0.42 (−0.46)

0.08 (0.78)

0.81 (−0.77)

0.28 (0.17)

0.75 (−0.67)

0.20 (−4.17)

0.08 (−0.16)

SEMA

1.52 (1.55)

0.69 (−0.15)

0.43 (1.24)

2.44 (1.07)

0.04 (−0.27)

0.07 (−1.02)

0.04 (1.21)

0.44 (−1.23)

0.35 (0.55)

0.90 (−2.40)

0.11 (−2.32)

0.41 (0.86)

SC12

0.22 (−0.06)

2.13 (0.12)

2.99 (0.17)

11.18 (0.19)

0.47 (−0.46)

0.17 (−0.39)

0.00 (0.00)

0.06 (0.07)

0.04 (−0.30)

1.45 (0.26)

0.05 (0.09)

0.00 (−0.01)

PNS24

3.58 (0.45)

0.49 (0.40)

0.40 (0.38)

105.99 (0.65)

1.57 (−1.10)

0.04 (−0.48)

0.04 (0.12)

0.27 (−0.06)

0.27 (−0.34)

0.08 (0.01)

1.00 (0.86)

1.27 (−0.74)

AGECL_BB

2.75 (−0.81)

0.30 (−0.78)

0.67 (−0.83)

1.30 (−0.48)

0.11 (−0.22)

0.12 (−0.23)

0.04 (0.12)

0.17 (−0.09)

0.84 (0.29)

0.00 (0.01)

0.25 (−4.97)

0.79 (−0.99)

AGECL_TC

0.04 (−0.06)

0.14 (−0.14)

1.49 (−1.11)

0.86 (−0.03)

0.04 (0.15)

0.05 (−1.29)

0.05 (1.45)

0.61 (−1.78)

0.00 (0.09)

0.20 (−0.33)

0.14 (−3.09)

0.66 (0.88)

PPAI_BB

0.58 (−0.99)

1.10 (−1.85)

0.24 (−1.07)

0.71 (−0.71)

0.00 (−0.10)

0.62 (0.23)

0.00 (0.31)

0.19 (−0.23)

0.57 (−2.78)

0.17 (0.25)

0.14 (−2.88)

0.49 (−2.89)

PPAI_TC

0.77 (−0.56)

0.11 (−0.35)

0.21 (−0.52)

5.11 (−1.46)

0.74 (1.33)

0.36 (−0.53)

0.09 (1.98)

0.91 (−2.18)

1.01 (1.78)

0.20 (−0.26)

0.18 (−3.73)

0.67 (−3.70)

  1. For each cell the first value is -log10 of the P-value for the annotation class and trait. The second value (in brackets) is the regression coefficient for annotation class and trait. Enriched annotations have positive effects, depleted annotations have negative effects.