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Table 4 Annotation of genome-wide significant SNPs (P value < 1.58E-06) associated with EN3

From: Genome-wide association analysis of egg production performance in chickens across the whole laying period

SNP

GGAa

Positionb

ALT/REFc

MAFd

Beta (SE)e

P value

Consequence

Candidate/ Nearest gene

rs14878430

1

117,871,938

C/T

0.407

0.25 (0.05)

7.96E-07

Intron

POLA1

rs14878446

1

117,881,774

T/C

0.408

0.25 (0.05)

1.38E-06

Intron

POLA1

rs313573834

1

117,885,299

A/G

0.408

0.25 (0.05)

1.38E-06

Intron

POLA1

rs13685872

1

117,898,459

A/G

0.417

0.25 (0.05)

1.04E-06

Intron

POLA1

rs316686965

1

117,904,908

T/A

0.417

0.25 (0.05)

9.65E-07

Intron

POLA1

rs314132663

1

117,907,038

A/G

0.408

0.25 (0.05)

1.38E-06

Intron

POLA1

rs314631582

1

117,939,090

C/T

0.406

0.26 (0.05)

7.05E-07

Intron

POLA1

rs315777735

1

117,943,070

A/G

0.418

0.27 (0.05)

1.19E-07

Intron

POLA1

rs13927842

1

118,028,676

C/A

0.426

0.26 (0.05)

4.70E-07

Intron

POLA1

rs317157084

1

118,046,119

C/T

0.426

0.26 (0.05)

4.70E-07

Downstream_43.27Kb

PDK3

rs14878614

1

118,062,286

C/A

0.426

0.26 (0.05)

4.70E-07

Downstream_27.35Kb

PDK3

rs313935473

1

118,272,993

A/G

0.423

0.24 (0.05)

1.45E-06

Upstream_3.672Kb

APOO

rs312874750

1

118,313,008

G/A

0.424

0.25 (0.05)

7.67E-07

Downstream_5.72Kb

APOO

rs312668110

1

118,340,009

G/C

0.433

0.25 (0.05)

6.31E-07

Intron

ACOT9

rs317511781

1

118,344,902

T/G

0.433

0.25 (0.05)

6.31E-07

Downstream_86bp

ACOT9

rs313236049

1

118,364,746

C/T

0.451

0.26 (0.05)

1.51E-07

Upstream_5.44Kb

PRDX4

  1. aChicken chromosome; bGallus_gallus-5.0 source; cALT/REF: alternative allele/reference allele; dMinor allele frequency; eEstimated allelic substitution effect per copy of the effect allele based on an inverse-normal transformed scale under an additive model, expressed in SD unit/allele