Table 1 Genes in linkage disequilibrium with the top 20 SNPs (features) in principal component 1 and 2 of principal component analysis involving Vrindavani cattle and its parental breeds.

From: Genome wide locus-specific ancestry analysis revealed adaptive admixtures in crossbred cattle of India

Principal component 1

Principal component 2

Chr

SNP

Position

Genes linked

to SNP

Feature loading

score

Chr

SNP

position

Genes linked

to SNP

Feature loading

score

3

15,818,013

KCNN3

2.77819

3

110,272,602

MAP7D1, TRAPPC3,

COL8A2

3.58398

3

32,316,119

DENND2D, CEPT1

2.77441

3

62,196,445

-

3.25334

4

53,050,980

-

2.82218

3

90,692,920

-

3.21352

4

34,669,189

LOC781830

2.75179

4

77,635,835

NUDCD3,

LOC104972146

3.43166

6

77,145,240

-

2.77703

5

66,157,408

LOC104972477,

CCDC53

3.43206

8

20,364,722

ELAVL2

2.79931

5

24,451,576

TMCC3

3.28886

10

72,846,830

-

2.74764

6

94,589,635

LOC107131184

3.87454

10

25,907,293

RPGRIP1, LOC107132837

2.74107

6

70,320,611

SCFD2

3.47473

11

85,097,357

LOC104973452

2.78714

6

52,371,211

-

3.32266

13

77,635,899

PREX1

2.7456

6

71,421,017

PDGFRA

3.25643

15

82,335,513

CTNND1, ZDHHC5

2.7975

7

45,383,502

CIRBP, C7H19orf24,

MUM1, LOC104969177

3.37343

16

4,061,366

SRGAP2

2.74541

7

48,376,442

H2AFY

3.33401

17

36,339,293

LOC107131163

2.83632

8

104,971,314

ZNF618

3.21094

18

16,070,657

PHKB

2.91285

9

65,564,012

TBX18

3.60243

20

14,290,727

ADAMTS6

2.76776

14

19,290,077

LOC100139328

3.48735

21

33,439,863

LINGO1

2.73207

16

27,894,801

TP53BP2

3.49402

22

53,470,362

TDGF1, LRRC2

2.7348

16

32,681,586

KIF26B

3.31581

22

53,457,282

RTP3

2.73451

22

19,168,846

GRM7

3.39106

24

34,876,101

MIB1

2.75379

26

37,797,893

VAX1

3.2925

24

37,194,377

-

2.74442

29

22,853,469

ANO5,

LOC104976236

3.47477

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