Table 3 The 29 significant and most distinct (> 50% unique SNPs and participants) genotype-lipidome relations.

From: Uncovering the complex genetic architecture of human plasma lipidome using machine learning methods

Relation ID

Number of shared participants

Number of SNPs

Number of independent SNPs

Number of lipid species

Hypergeometric p-value

Associated clinical variables (p-value)*

R9

62

1447

1191

17

5.1 × 10−19

TC (0.0002), Systolic BP (0.0001), diastolic BP (0.0005), LDL-C (0.002)

R7

29

1447

1191

14

1.2 × 10−13

TC (0.02), systolic BP (7 X 10−06), diastolic BP (0.0008), LDL-C (0.04), Blood glucose (0.02)

R5

46

1447

1191

22

4.0 × 10−09

TG (0.01), CRP (0.02), Systolic BP (0.0001), diastolic BP (2.4 X 10−06)

R68

27

27

17

82

3.1 × 10−06

TC (0.001), HDL C (0.0002), TG (0.002), diastolic BP (0.04), LDL-C (0.0006), blood insulin (0.03)

R1

25

1447

1191

11

8.6 × 10−06

HDL C (0.03)

R184

21

12

4

82

1.7 × 10−05

BMI (0.01), HDL-C (0.0003), TG (0.003), blood glucose (0.01), blood insulin (0.01)

R107

7

232

173

30

4.2 × 10−05

HDL-C (0.03), TG (0.03), systolic BP (0.002), diastolic BP (0.02)

R162

6

54

28

12

1.6 × 10−04

TC (4 X 10−05)

R119

9

34

19

30

4.6 × 10−04

HDL-C (0.001), TG (0.007), diastolic BP (0.05)

R103

5

193

123

28

4.7 × 10−04

TG (0.006)

R156

6

90

45

14

6.0 × 10−04

TG (0.005)

R101

11

8

2

82

6.2 × 10−04

TC (0.01), HDL-C (0.01), LDL-C (0.04)

R93

7

50

9

17

7.3 × 10−04

Systolic BP (0.05), diastolic BP (0.05), LDL-C (0.05)

R188

14

19

3

22

8.3 × 10−04

-

R57

9

19

7

30

9.9 × 10−04

TG (0.02)

R153

7

13

3

82

1.5 × 10−03

TC (0.008), HDL-C (0.04), LDL-C (0.004)

R94

5

7

3

23

1.7 × 10−03

TC (0.04), TG (0.05)

R32

15

65

24

82

2.1 × 10−03

TC (0.01), LDL-C (0.02), blood glucose (0.006), blood insulin (0.02)

R89

8

38

16

30

3.2 × 10−03

Systolic BP (0.003)

R10

16

1447

1191

10

3.6 × 10−03

systolic BP (0.05), diastolic BP (0.008), blood insulin (0.005)

R181

7

14

1

16

3.7 × 10−03

-

R45

11

114

62

16

4.0 × 10−03

HDL-C (0.003), diastolic BP (0.02)

R6

11

1447

1191

14

6.1 × 10−03

Systolic BP (0.02), diastolic BP (0.004)

R8

17

1447

1191

28

6.1 × 10−03

TC (0.03)

R58

5

19

7

29

6.6 × 10−03

TG (0.04), CRP (0.05), blood glucose (0.03)

R0

23

59

24

82

7.1 × 10−03

BMI (0.01), TC (0.008), HDL-C (0.0001), TG (3.8 X 10−07)

R3

22

1447

1191

19

7.9 × 10−03

TC (0.03), LDL-C (0.04)

R164

7

10

2

16

8.1 × 10−03

BMI (0.004)

R104

5

10

1

36

9.9 × 10−03

HDL-C (0.05), TG (0.02), blood insulin (0.009)

  1. Explanations of table columns 2nd column, number of shared participants between genotype and lipidome biclusters; 3rd and 4th columns, number of SNPs in the genetic bicluster before and after linkage disequilibrium (LD)-based SNP pruning respectively; 5th column, number of lipid species in the lipid bicluster; 6th column, hypergeometric p-values for the overlap of participants in the genotype and lipidome biclusters of the relation; 7th column, clinical variables with respect to which the participants in the genetic biclusters of the corresponding genotype-lipidome relations are significantly (p-values in parentheses) different as compared to the rest of the participants assessed with *two-sample t-test. TC Total cholesterol; HDL-C high density lipoprotein cholesterol; LDL-C Low density lipoprotein cholesterol; CRP C-reactive protein; TG Triglycerides; BP Blood pressure.
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