Table 2 Markers showing genome wide significant associations with test day fat percentage (TFP).

From: High density genome wide genotyping-by-sequencing and association identifies common and low frequency SNPs, and novel candidate genes influencing cow milk traits

Marker

Chr

Position

RS or SS number

Classification

Gene/(nearby gene (s)) 1

Minor/Major Allele

P-Value 2

P-Value 2 BH FDR

Proportion Variance Explained

MAF 3

Additive and dominant models

 S14_1074199

14

1074199

rs210334336

Intergenic

(GRINA, Them6)

T/G

2.09E-13 (1.53E-11)

1.4E-08 (3.8E-07)

0.0657

0.288

 S14_392338

14

392338

rs209328075

Intergenic

(CPSF1)

T/C

3.72E-13 (6.99E-12)

1.4E-08 (2.6E-07)

0.0644

0.276

 S14_412791

14

412791

rs135576599

Intronic

ADCK5

G/A

1.22E-12 (1.54E-14)

3E-08 (1.1E-09)

0.0616

0.259

 S14_714848

14

714848

rs207501095

Intergenic

(MIR2309)

G/A

6.83E-11 (3.5E-10)

1.3E-06 (5.2E-06)

0.0522

0.307

 S14_277266

14

277266

rs135581384

Intronic

TONSL

G/A

2.4E-10 (2.7E-11)

3.6E-06 (5E-07)

0.0493

0.257

 S14_271158

14

271158

rs132685115

Intronic

TONSL

T/C

1.19E-09 (3.54E-08)

1.5E-05 (0.0004)

0.0455

0.271

 S14_714785

14

714785

rs210191478

Intergenic

(MIR2309)

A/G

9.64E-09 (6.43E-09)

0.0001 (7.9E-05)

0.0406

0.315

 S14_1092614

14

1092614

rs110638778

Intergenic

(GRINA, Them6)

A/G

5.09E-08 (1.68E-07)

0.00047 (0.00139)

0.0367

0.374

 S14_705269

14

705269

rs210465271

Intergenic

(MIR2309)

C/T

2.1E-07 (6.76E-07)

0.00173 (0.00501)

0.0334

0.305

 S14_3449027

14

3449027

rs133123595

Intergenic

—

G/A

1.14E-06 (2.79E-06)

0.00843 (0.01478)

0.0294

0.28

 S11_103120099

11

103120099

rs137050272

Intergenic

(PPP2R4, IER5L)

G/A

1.69E-06 (1.28E-07)

0.01137 (0.00119)

0.0285

0.023

 S14_707436

14

707436

rs436930795

Intergenic

(MIR2309)

G/A

2.17E-06 (1.43E-06)

0.01235 (0.0088)

0.0279

0.289

 S14_707458

14

707458

rs470862327

Intergenic

(MIR2309)

C/T

2.17E-06 (1.43E-06)

0.01235 (0.0088)

0.0279

0.289

 S14_215462

14

215462

rs133629644

Intronic

PPP1R16A

A/G

4.14E-06 (2.58E-06)

0.0192 (0.0147)

0.0264

0.262

 S22_60211708

22

60211708

ss1850244253

Intergenic

—

T/G

4.73E-06 (2.13E-05)

0.02061 (0.0686)

0.0261

0.068

 S3_108393170

3

108393170

rs445966307

Intronic

PTPRF

C/A

1.52E-05 (1.52E-05)

0.0564 (0.05936)

0.0233

0.018

 S14_3590983

14

3590983

rs381816253

Intergenic

—

G/C

1.86E-05 (2.61E-05)

0.06276 (0.07735)

0.0228

0.381

 S14_3590986

14

3590986

rs207862021

Intergenic

—

T/G

1.86E-05 (2.61E-05)

0.06276 (0.07735)

0.0228

0.381

 S20_2735814

20

2735814

ss1850214424

Intergenic

—

C/A

2.29E-05 (2.79E-05)

0.0707 (0.0796)

0.0223

0.015

 S14_3016578

14

3016578

rs110049376

Intergenic

(KCNK9)

G/A

2E-05 (6.39E-06)

0.06434 (0.03156)

0.0227

0.271

 S17_11520990

17

11520990

ss1850176355

Intronic

EDNRA

G/T

2.63E-05 (1.68E-05)

0.07789 (0.06208)

0.022

0.018

 S27_14944791

27

14944791

ss1850284750

Intergenic

(ODZ3, DCTD)

C/T

3.03E-05 (1.88E-05)

0.0832 (0.0633)

0.0217

0.021

Additive model

 S14_1092930

14

1092930

ss1850142751

Intergenic

(GRINA, Them6)

C/T

3.04E-06

0.01608

0.0271

0.37

 S14_1028006

14

1028006

rs109714772

Intergenic

(GSDMD, GRINA)

G/A

5.08E-06

0.02091

0.0259

0.383

 S10_26036745

10

26036745

ss1850090958

Coding 4

TEP1

C/A

1.23E-05

0.04808

0.0238

0.016

 S21_34082280

21

34082280

ss1850229276

Intronic

EDC3

G/T

3.58E-06

0.01771

0.0267

0.015

 S20_38406577

20

38406577

rs466001634

Intergenic

(EGFLAM, GDNF)

G/A

2.94E-05

0.0832

0.0218

0.216

Dominant model

 S5_1569102

5

1569102

rs436392082

Intergenic

(RAB21)

A/G

3.86E-05

0.0951

0.0211

0.024

 S5_1569121

5

1569121

rs382849766

Intergenic

(RAB21)

G/T

3.38E-05

0.08941

0.0214

0.024

 S14_1666599

14

1666599

rs207822284

Intergenic

(LY6H)

T/C

3.98E-05

0.0951

0.0211

0.294

 S14_2513747

14

2513747

rs207542860

Intronic

TRAPPC9

T/C

7.08E-06

0.03279

0.0251

0.335

 S29_9009252

29

9009252

ss1850314769

Intergenic

(FZD4, PRSS23)

C/T

1.78E-05

0.06289

0.0229

0.37

 S17_48121597

17

48121597

rs109745026

Intergenic

—

A/G

1.25E-05

0.05437

0.0238

0.195

 S13_74353017

13

74353017

ss1850139198

Intronic

MATN4

C/A

3.83E-05

0.0951

0.0211

0.045

 S2_78485721

2

78485721

ss1849982270

Intergenic

—

C/A

3.35E-05

0.08941

0.0215

0.017

 S1_146045552

1

146045552

rs466469615

Intergenic

—

T/C

1.4E-05

0.05758

0.0235

0.027

  1. 1Near by genes are within 1Mbp of surrounding regions.
  2. 2Figures in brackets were obtained with the dominant model.
  3. 3MAF, Minor allele frequency.
  4. 4S10_26036745 (ss1850090958) (c.3017A>C, p.Tyr1006Ser, exon 3).
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