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Table 6 Functional annotation of SNP identified in the 14 positional candidate genes, from sequencing data of 28 parental chickens of the Embrapa F2 Chicken Resource Population

From: Genome-wide association scan for QTL and their positional candidate genes associated with internal organ traits in chickens

Genetic variants annotation Positional candidate genes
PTPN11 RB1 TNFSF11 ITGB4 SLC6A4 GTF2F2 SPERT KCTD4 HTR2A PCDH7 LCORL LDB2 NR4A2 GPD2
3′ UTR1 20 10 6 5 3 14
5′ UTR2 1 2 1 1
Downstream 57 94 104 127 70 129 54 80 60 16 127 80 83 88
Intron 290 1431 332 436 150 1849 13 404 1789 811 3138 14 490
Non-synonymous 2 3 9 4 1 7
Splice region (synonymous) 3 2 1
Splice region (intron) 2 3 8
Synonymous 5 15 4 49 11 2 2 1 3 7 1 16 8
Upstream 97 101 90 296 89 90 66 106 64 12 52 42 60 35
Total 452 1668 533 928 326 2081 135 193 531 1825 995 3264 196 621
  1. 1Within 5 kb downstream of the 3 prime end of a transcript
  2. 2Within 5 kb upstream of the 5 prime end of a transcript