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Table 3 SNPs significantly associated with RFI

From: Combination analysis of genome-wide association and transcriptome sequencing of residual feed intake in quality chickens

Locus Chr Positiona Effectb P-valuec MAFd Var(%)e Nearest gene SNP-gene relation
rs313001261 1 47140273 0.35 4.08E-05 0.36 9.52 SLC17A8 UTR-3
rs14820118 1 47142175 0.34 8.75E-05 0.35 8.53 SLC17A8 downstream
rs313802356 2 81015541 −0.44 6.90E-05 0.16 2.24 COBL UTR-3
rs316977875 2 81047713 −0.44 6.37E-05 0.16 2.24 COBL intron
rs312370583 2 81093795 −0.44 7.73E-05 0.16 2.42 COBL intron
rs312326618 4 5197844 −0.3 7.60E-05 0.44 4.8 PCDH19 intron
rs316570003 4 78962129 0.38 8.13E-05 0.22 9.71 JAKMIP1 intron
rs14494646 4 79000778 0.44 9.74E-05 0.13 6.93 JAKMIP1 upstream
rs312925954 4 82293366 0.45 1.76E-05 0.16 4.52 ZFYVE28 intron
rs16445177 4 82306738 0.4 5.39E-05 0.18 4.29 ZFYVE28 intron
rs312767762 9 4440306 −0.53 7.90E-05 0.1 8.43 PPP1R7 intron
rs16663153 9 4507514 −0.51 6.10E-05 0.11 8.13 SEPT2 downstream
rs14046165 12 16386012 0.33 4.20E-05** 0.38 4.15 RYBP intron
rs312899555 12 16393667 0.33 5.37E-05** 0.31 2.63 RYBP intron
rs313947867 12 16400923 0.33 4.28E-05** 0.31 2.63 RYBP intron
rs317049993 12 16423468 0.32 3.39E-05** 0.4 4.38 RYBP upstream
rs315004580 12 16640380 0.32 3.00E-05* 0.47 5.54 PDZRN3 intron
rs315162282 12 16648446 0.32 3.27E-05* 0.47 5.54 PDZRN3 intron
rs317287197 12 16660649 0.32 2.66E-05* 0.47 5.54 PDZRN3 intron
rs316098097 12 16673403 0.32 3.86E-05** 0.47 5.54 PDZRN3 intron
rs314131263 12 16681057 0.32 3.45E-05** 0.47 5.62 PDZRN3 intron
rs14046530 12 16758193 −0.32 6.89E-05** 0.49 4.54 PDZRN3 upstream
rs315238546 12 17083942 0.3 5.60E-05** 0.41 5.94 LOC101749255 downstream
rs315693318 12 17089689 0.3 8.62E-05** 0.41 5.94 LOC101749255 downstream
rs315157887 12 17160768 0.37 3.92E-06** 0.38 7.41 LOC101749255 upstream
rs317584843 12 17195875 0.32 6.31E-05** 0.3 5.22 CHL1 upstream
rs314285248 12 17230860 0.33 6.92E-06** 0.46 5.08 CHL1 intron
rs317278144 12 17239654 0.35 3.34E-05* 0.25 7.47 CHL1 intron
rs317188563 12 17260556 0.28 8.02E-05** 0.5 1.88 CHL1 intron
rs316897066 18 3599249 0.28 7.54E-05 0.44 5.18 UTS2R downstream
rs315285389 23 1733290 −0.38 2.27E-05* 0.24 3.39 ZMPSTE24 upstream
rs315491506 26 3777283 −0.38 2.65E-05 0.21 9.28 SYT6 intron
  1. aPhysical position
  2. bAdditive effect of allele B (minor allele)
  3. c P-value corrected for inflation factor λ, *FDR ≤10 %, ** FDR ≤5 %
  4. dMinor allele frequency
  5. eThe proportion of the phenotypic variance accounted by the SNP
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