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Table 3 SNPs significantly associated with RFI

From: Combination analysis of genome-wide association and transcriptome sequencing of residual feed intake in quality chickens

Locus

Chr

Positiona

Effectb

P-valuec

MAFd

Var(%)e

Nearest gene

SNP-gene relation

rs313001261

1

47140273

0.35

4.08E-05

0.36

9.52

SLC17A8

UTR-3

rs14820118

1

47142175

0.34

8.75E-05

0.35

8.53

SLC17A8

downstream

rs313802356

2

81015541

−0.44

6.90E-05

0.16

2.24

COBL

UTR-3

rs316977875

2

81047713

−0.44

6.37E-05

0.16

2.24

COBL

intron

rs312370583

2

81093795

−0.44

7.73E-05

0.16

2.42

COBL

intron

rs312326618

4

5197844

−0.3

7.60E-05

0.44

4.8

PCDH19

intron

rs316570003

4

78962129

0.38

8.13E-05

0.22

9.71

JAKMIP1

intron

rs14494646

4

79000778

0.44

9.74E-05

0.13

6.93

JAKMIP1

upstream

rs312925954

4

82293366

0.45

1.76E-05

0.16

4.52

ZFYVE28

intron

rs16445177

4

82306738

0.4

5.39E-05

0.18

4.29

ZFYVE28

intron

rs312767762

9

4440306

−0.53

7.90E-05

0.1

8.43

PPP1R7

intron

rs16663153

9

4507514

−0.51

6.10E-05

0.11

8.13

SEPT2

downstream

rs14046165

12

16386012

0.33

4.20E-05**

0.38

4.15

RYBP

intron

rs312899555

12

16393667

0.33

5.37E-05**

0.31

2.63

RYBP

intron

rs313947867

12

16400923

0.33

4.28E-05**

0.31

2.63

RYBP

intron

rs317049993

12

16423468

0.32

3.39E-05**

0.4

4.38

RYBP

upstream

rs315004580

12

16640380

0.32

3.00E-05*

0.47

5.54

PDZRN3

intron

rs315162282

12

16648446

0.32

3.27E-05*

0.47

5.54

PDZRN3

intron

rs317287197

12

16660649

0.32

2.66E-05*

0.47

5.54

PDZRN3

intron

rs316098097

12

16673403

0.32

3.86E-05**

0.47

5.54

PDZRN3

intron

rs314131263

12

16681057

0.32

3.45E-05**

0.47

5.62

PDZRN3

intron

rs14046530

12

16758193

−0.32

6.89E-05**

0.49

4.54

PDZRN3

upstream

rs315238546

12

17083942

0.3

5.60E-05**

0.41

5.94

LOC101749255

downstream

rs315693318

12

17089689

0.3

8.62E-05**

0.41

5.94

LOC101749255

downstream

rs315157887

12

17160768

0.37

3.92E-06**

0.38

7.41

LOC101749255

upstream

rs317584843

12

17195875

0.32

6.31E-05**

0.3

5.22

CHL1

upstream

rs314285248

12

17230860

0.33

6.92E-06**

0.46

5.08

CHL1

intron

rs317278144

12

17239654

0.35

3.34E-05*

0.25

7.47

CHL1

intron

rs317188563

12

17260556

0.28

8.02E-05**

0.5

1.88

CHL1

intron

rs316897066

18

3599249

0.28

7.54E-05

0.44

5.18

UTS2R

downstream

rs315285389

23

1733290

−0.38

2.27E-05*

0.24

3.39

ZMPSTE24

upstream

rs315491506

26

3777283

−0.38

2.65E-05

0.21

9.28

SYT6

intron

  1. aPhysical position
  2. bAdditive effect of allele B (minor allele)
  3. c P-value corrected for inflation factor λ, *FDR ≤10 %, ** FDR ≤5 %
  4. dMinor allele frequency
  5. eThe proportion of the phenotypic variance accounted by the SNP
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BMC Genomics

ISSN: 1471-2164

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