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Table 4 Annotation of SNPs with significance associated with egg number traits in 627 of line W2 hens

From: A significant quantitative trait locus on chromosome Z and its impact on egg production traits in seven maternal lines of meat-type chicken

Traitsa rs GGAb Positionc Allele AF βd P-value Gene Gap, kbe
EN2 rs315536207 24 4,203,575 G/A 0.41 −0.84 4.84E-06 THY1 Instron
EN2 rs316053320 Z 10,263,677 A/G 0.11 −1.00 4.60E-06 ADAMTS12 Instron
EN2, EN3, TEN rs318154184 Z 10,661,667 T/A 0.46 1.97 4.08E-06 PRLR Instron
EN2, EN3, TEN rs13769886 Z 10,672,563 G/C 0.46 1.97 4.08E-06 PRLR Instron
EN2, EN3, TEN rs313325646 Z 10,706,318 A/G 0.46 1.97 4.08E-06 PRLR U 26.6 KB
EN2, TEN rs317829338 Z 11,039,011 C/A 0.11 −1.07 3.92E-07 RANBP3L Instron
EN2, TEN rs317316870 Z 11,049,964 C/G 0.11 −1.07 3.92E-07 NADK2 U 25.3 KB
EN2, TEN rs16130829 Z 11,138,239 G/A 0.11 −1.04 7.72E-07 SLC1A3 D 34.0 KB
EN2, TEN rs313925951 Z 11,181,202 A/G 0.11 −1.04 7.72E-07 SLC1A3 Instron
EN2, TEN rs315242894 Z 11,250,945 G/A 0.11 −1.04 7.72E-07 SLC1A3 U 16.7 KB
EN2, TEN rs315141712 Z 11,295,727 G/A 0.11 −1.04 7.72E-07 SLC1A3 D 58.6 KB
EN2, TEN rs313907922 Z 11,336,593 A/G 0.1 −0.97 3.87E-06 SLC1A3 D 98.5 KB
EN2, TEN rs314230546 Z 11,360,621 T/A 0.12 −1.03 8.51E-07 CPLANE1 D 106.3 KB
EN2, TEN rs316797236 Z 11,583,068 T/A 0.09 −1.06 1.39E-06 WDR70 Instron
EN2, TEN rs318193135 Z 11,775,041 A/G 0.09 −1.12 3.46E-07 GDNF U 30.6 KB
EN2, TEN rs14786300 Z 11,823,333 A/G 0.09 −1.12 3.46E-07 GDNF U 77.9 KB
EN2, TEN rs14786270 Z 11,831,103 G/A 0.09 −1.12 3.46E-07 GDNF U 85.5 KB
EN2, TEN rs14786427 Z 11,995,193 A/G 0.09 −1.13 6.28E-07 EGFLM D 2.7 KB
EN2, TEN rs317925374 Z 12,003,955 T/A 0.1 −1.03 1.23E-06 LIFR D 3.33 KB
EN2, TEN rs16131724 Z 12,481,249 A/G 0.12 −1.07 2.36E-07 DAB2 U 117.9 KB
EN2, TEN rs317751736 Z 12,614,891 A/G 0.12 −1.07 2.36E-07 OTGER4 D 219.8 KB
EN2 rs14756086 Z 12,901,024 G/A 0.16 −0.84 2.22E-06 PRKAA1 Instron
EN2, TEN rs317744265 Z 12,965,710 A/G 0.11 −1.03 7.63E-07 C6 D 0.7 KB
EN2 rs14756790 Z 13,656,667 A/G 0.13 −0.93 1.40E-06 HMGCS1 Instron
EN2 rs316455929 Z 13,662,376 A/G 0.13 −0.93 1.40E-06 HMGCS1 Instron
EN2 rs313666070 Z 79,095,862 G/A 0.26 0.63 6.28E-06 FEM1C D 22.0 KB
EN3 rs14485191 4 66,642,445 A/G 0.22 −3.06 3.29E-06 CORIN Instron
EN3 rs318004733 4 66,681,294 G/A 0.22 −3 4.29E-06 CORIN Instron
TEN, EN4 rs14319456 3 6,449,298 G/A 0.2 −0.92 2.11E-05 NRXN1 D 706.6 KB
  1. aEN2, EN3, EN4, and TEN represent egg numbers at four stages (from 196 to 227 d, from 228 to 307 d, from 308 to 354 d, and from onset of laying eggs to 354 d, respectively)
  2. bGallus gallus chromosome
  3. cGallus_gallus-6.0 source
  4. dAllele substitution effect was the additive effect estimated by GEMMA
  5. eU and D indicate that the SNP is upstream and downstream of a gene, respectively