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Table 1 Peak variants for FT-MIR wavenumbers with highly significant protein sequence association effects

From: Sequence-based genome-wide association study of individual milk mid-infrared wavenumbers in mixed-breed dairy cattle

Chr

Position

Tag variant ID

N of hits

Top wvn (cm−1)

Iter

P-value

Protein coding variant ID

LD

Gene

Impact

Description

3

7908611

rs137763930

11

940

1

6.7e−20

rs110560331

0.976

FCRLA

L

c.233-3 T > C

3

7931694

rs211402696

20

1462

2

1.2e−23

rs381714237

0.989

FCGR2B

H

c.899dupC

3

15411459

rs134900385

6

1022

1

4.3e−19

rs382689947

0.994

FAM189B

M

c.1237 T > C

3

15411459

rs134900385

6

1022

1

4.3e−19

rs134844772

0.990

GBA

M

c.1080C > A

3

15411459

rs134900385

6

1022

1

4.3 e−19

rs132659643

0.999

HCN3

M

c.1699A > G

3

15411459

rs134900385

6

1022

1

4.3e−19

rs109330809

0.990

MTX1

L

c.508-6 T > C

3

15517871

rs109328483

6

1007

1

4.4e−19

rs136761456

0.992

SCAMP3

M

c.151G > C

3

15517871

rs109328483

6

1007

1

4.4e−19

rs43706482

0.994

THBS3

L

c.2075-3 T > C

3

15550598

rs380597285

327

1462

0

1.3e−54

rs109816684

0.994

SLC50A1

L

c.282 + 7G > A

5

75729880

rs384734208

50

1466

1

5.0e−47

rs207628090

0.930

CSF2RB

M

c.41 T > C

5

75758989

rs210094995

2

1447

0

5.8e−40

rs210937722

0.926

NCF4

M

c.841G > C

5

118246868

rs136859160

308

1261

0

3.0e−44

rs456403270

0.937

TBC1D22A

M

c.1063C > T

6

38027010

rs43702337

455

1119

0

7.3e−948

rs43702337

1

ABCG2

M

c.1742A > C

6

87181619

rs43703011

17

3633

2

2.5e−22

rs43703011

1

CSN2

M

c.245C > A

6

87274397

rs378808772

3

1283

2

9.9e−51

rs43703010

0.974

CSN1S1

M

c.620A > G

6

87390576

rs43703015

18

1473

1

4.0e−108

rs43703015

1

CSN3

M

c.470 T > C

11

103304757

rs109625649

329

1593

0

1.2e−134

rs109625649

1

PAEP

M

c.401 T > C

11

104242578

rs207688357

11

1462

0

5.5e−33

rs207688357

1

ABO

H

c.233 + 1G > C

12

69612955

rs383509255

132

1716

0

6.4e−45

rs208744187

0.950

TGDS

M

c.204A > C

14

1726650

rs133611586

6

3514

1

1.6e−75

 

0.992

WDR97

L

c.2656-5_2656-4insG

14

1732043

rs437406031

384

2846

1

6.3e−42

rs450710918

0.990

ENS..39978

M

c.352G > A

14

1732043

rs437406031

384

2846

1

6.3e−42

rs476736066

0.997

MROH1

M

c.3549G > C

14

1755742

rs384226556

5

2656

0

4.0e−20

rs209542297

0.9998

CPSF1

L

c.4287 T > C

14

1802265

rs109234250

310

1716

0

1.5e−2607

rs109234250

1

DGAT1

M

c.694G > A

14

1802265

rs109234250

310

1716

0

1.5e−2607

rs134364612

0.999

SLC52A2

M

c.724A > G

14

66328304

rs446084949

19

1029

1

2.7e−20

rs446084949

1

SPAG1

M

c.2044G > A

15

28347165

rs210034037

5

1537

0

7.7e−35

rs208325660

0.999

RNF214

M

c.314G > A

15

53940444

rs382926661

23

1205

1

4.2e−19

rs380220394

0.993

DNAJB13

L

c.69-4 T > C

16

24977696

rs111027377

62

2742

2

4.8e−25

rs109896036

0.988

MTARC1

L

c.628-5C > T

16

24977696

rs111027377

62

2742

2

4.8e−25

rs110899826

0.988

MTARC1

M

c.581C > G

19

42428366

rs209808022

4

1250

1

3.1e−25

rs209302038

0.991

KRT9

M

c.196C > T

19

42488389

rs379667889

8

1447

0

7.8e−34

rs209756857

0.969

KRT42

L

c.57 + 7C > T

19

42488389

rs379667889

8

1447

0

7.8e−34

rs383013355

0.963

KRT16

M

c.896A > G

19

42488389

rs379667889

8

1447

0

7.8e−34

rs208923483

0.966

KRT17

M

c.146G > C

19

42488389

rs379667889

8

1447

0

7.8e−34

rs385937063

0.966

KRT17

L

c.1233C > T

19

43036265

rs210324533

11

1029

1

5.3e−43

rs207799702

0.944

KAT2A

L

c.700-7C > G

19

43036265

rs210324533

11

1029

1

5.3e−43

rs209410283

0.945

KCNH4

M

c.408C > G

19

43036265

rs210324533

11

1029

1

5.3e−43

rs377779402

0.945

KCNH4

H

c.2663 + 2 T > C

19

43053995

rs481837688

24

1212

1

6.6e−26

rs481837688

1

STAT5A

M

c.2305C > A

19

51303887

rs41921224

65

1499

0

1.9e−35

rs41921160

0.993

CCDC57

M

c.1907 T > C

19

57087981

rs41920620

6

1216

0

1.8e−21

rs469721022

0.999

HID1

L

c.1147-7G > C

28

6559147

rs133101552

3

1261

0

8.6e−23

rs133101552

1

KCNK1

M

c.934C > A

29

41821270

rs207854419

14

1257

1

4.6e−30

rs384900272

0.998

NXF1

M

c.1555G > A

  1. Peak variants and association effects for FT-MIR wavenumbers classified as highly significant. Highly significant effects are classified such that: the –log10(p-value) for the effect was greater than 1.5 × the Bonferroni threshold and the correlation between the tag variant and the protein sequence variant was in the range (0.975, 1]; or the –log10(p-value) for the effect was greater than 2 × the Bonferroni threshold and the correlation between the tag variant and the protein sequence variant was in the range (0.95, 0.975]; or the –log10(p-value) for the effect was greater than 2.5 × the Bonferroni threshold and the correlation between the tag variant and the protein sequence variant was in the range (0.925, 0.95]. Bonferroni threshold: –log10(6.2e–13). N of hits: number of wavenumbers for which the variant was selected as the representative (most significant) tag variant for a peak. Iterations are defined relative to the base GWAS, with the base GWAS represented as iteration 0. L Low impact splice region variant, M  Moderate impact missense variant, H High impact splice donor