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Table 2 The top 20 variants with the lowest p-values from the meta-analysis of genome wide associations studies from two resource populations (F2 and HS; half-sib) with the trait ‘posterior probability of a hen to belong to the extreme feather pecking subgroup’ (pEFP)

From: Meta-analyses of genome wide association studies in lines of laying hens divergently selected for feather pecking using imputed sequence level genotypes

Chr

Position (bp)

ID

p-value

Variant effect

Symbol

3

104,391,861

rs740633021

5.533E-08

intron / upstream gene

NRBP1 / LOC107053158 (ncRNA)

1

91,991,270

rs737049739

1.878E-07

intergenic

EPHA6

14

2,899,119

rs14070749

1.968E-07

non coding transcript / exon

LOC101750426 (ncRNA)

1

133,743,444

rs15428397

2.710E-07

intron

KIAA1211L

10

11,902,712

rs317563905

2.938E-07

downstream gene

SH3GL3 / LMINA

10

11,904,575

rs316617403

3.373E-07

downstream gene / 3 prime UTR

SH3GL3 / LMINA

10

11,901,170

rs315794181

3.564E-07

downstream gene / 3 prime UTR

SH3GL3 / LMINA

5

8,789,444

rs312755711

5.313E-07

intron, non coding transcript

LOC107053374 (ncRNA)

9

14,663,252

rs14674949

5.865E-07

intron

LPP

18

6,202,927

rs736783194

7.428E-07

intergenic

C18H17ORF67

2

48,074,231

2_48,074,231

9.747E-07

intron

PDE1C

11

16,848,616

rs732938021

0.000001084

intron

KLHL36

2

16,335,664

rs731673476

0.000001226

intron

MYO3A

13

8,132,912

rs739578589

0.000001461

intron

GABRB2

10

11,904,145

rs313724095

0.000001503

downstream gene / 3 prime UTR

SH3GL3 / LMINA

1

133,734,332

rs14889804

0.000001544

intron

KIAA1211L

1

133,762,004

rs13624872

0.000001753

intron

KIAA1211L

1

133,776,463

rs313923430

0.000002173

intron

TSGA10

1

133,733,974

rs1059691759

0.000002254

intron

KIAA1211L

6

29,989,563

6_29,989,563

0.000002303

intron

SHTN1