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Table 4 Contributions of six SNPs in genes potentially related to the total integral intensity

From: Genetic variations for the eggshell crystal structure revealed by genome-wide association study in chickens

SNP

Gene

Consequence

Chr.

Position (bp)

EA/AA

P

MAF

Beta (SE)

CPV (%)

rs314759160

PLCZ1

intron_variant

1

64,223,356

A/C

4.96E-10

0.454

-0.345(-0.055)

5.90

rs314403945

ITPR2

intron_variant

1

67,660,408

T/C

9.18E-09

0.475

0.320(-0.055)

5.11

rs312653027

IAPP

downstream_gene_variant

1

65,271,009

C/T

5.42E-09

0.443

-0.391(-0.054)

5.02

rs314985144

ABCC9

intron_variant

1

66,908,211

G/A

2.75E-08

0.468

-0.305(-0.054)

4.63

rs15301807

KCNJ8

intron_variant

1

66,959,507

A/C

3.52E-07

0.470

-0.285(-0.056)

4.05

rs315771606

CACNA1C

intron_variant

1

61,199,051

G/A

5.13E-07

0.468

-0.281(-0.056)

3.93

  1. Abbreviations: EA/AA: effect allele (minor allele)/alternative allele (major allele); EA = effect allele (minor allele); AA = alternative allele (major allele); MAF = minor allele frequency; CPV = contribution to phenotypic variance. Beta is the estimated allelic substitution effect per copy of the effect allele (EA) based on an inverse-normal transformed scale under an additive model, expressed in SD unit/allele; SE = standard error of the beta
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BMC Genomics

ISSN: 1471-2164

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