Table 1 Relationship classification between trait associated CNVs and their neighboring SNPs for 82 combinations of trait and CNVs

1

2.56E-06

2.12E-08

0.0246

0.0657

3.96E-21

IN*

IN*

IN*

NN

2

8.53E-07

1.32E-07

0.0020

0.8913

1.46E-09

IN

IN

IN

NN

Yes

3

0.0810

0.1375

0.9468

0.6499

1.32E-32

IN*

4

1.26E-09

1.99E-08

4.06E-09

0.1334

0.0756

IN**

IN**

IN**

Yes

5

0.2506

0.0473

0.2410

0.0758

0.0008

IN*

IN*

Yes

Yes

6

0.0008

1.91E-06

4.95E-05

0.0004

6.95E-22

NN

NN

IN

NN

NN

Yes

7

0.0020

0.0001

0.0418

0.2851

1.38E-05

IN**

IN**

NN

IN**

Yes

8

9.03E-10

5.38E-10

1.61E-06

1.0000

9.35E-05

IN*

IN*

IN*

IN*

Yes

9

0.0005

2.50E-06

0.2701

0.0049

9.47E-18

IN**

IN**

NN

IN

10

9.29E-12

8.38E-12

2.23E-07

1.0000

0.0997

IN

IN

IN*

11

3.81E-05

6.52E-05

0.0345

0.7610

0.0037

IN*

IN*

IN*

IN

Yes

Yes

12

0.0006

0.1336

0.5275

3.70E-09

1.52E-22

IN*

IN*

NN

Yes

14

0.1484

0.5341

0.7490

0.0700

0.0371

IN*

Yes

16

0.2552

0.8739

0.0352

0.0033

0.2416

NN

LD*

Yes

17

6.96E-07

2.87E-06

2.99E-05

0.4144

0.9401

IN*

IN**

IN*

Yes

18

0.0890

2.02E-05

0.0062

1.79E-13

6.21E-15

LD

LD

IN* + LD

IN*

Yes

Yes

19

0.0032

3.53E-05

0.2698

0.0061

0.0035

IN*

IN*

IN*

IN

Yes

20

0.9468

0.8614

0.6384

1.0000

0.0286

NN

21

0.0798

0.1692

0.5656

0.3360

0.0433

IN + LD

Yes

22

0.6780

0.4652

0.3753

0.9048

0.0005

NN

Yes

Yes

23

0.0065

0.0209

0.0008

0.5674

7.60E-05

NN

IN**

IN**

NN

24

0.0616

0.0844

0.6569

0.8919

6.98E-09

NN

Yes

Yes

25

4.43E-08

1.58E-08

1.94E-05

0.9206

0.4082

IN

IN**

IN**

26

0.8385

0.7831

0.8926

0.9465

2.51E-16

IN + LD

Yes

28

0.0016

1.70E-08

0.0008

2.21E-13

0.0002

LD* NS

LD* NS

LD* NS

IN* + LD

LD*

Yes

Yes

29

8.09E-07

2.03E-07

0.0007

0.7631

3.02E-05

IN + LD

IN + LD

IN + LD

NN

Yes

31

0.1197

0.0159

0.1152

0.0773

3.15E-05

IN

IN**

Yes

Yes

32

9.08E-09

3.95E-08

0.0001

0.5293

4.20E-07

LD NS

NN

LD

IN + LD