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Table 1 The overlap between eQTL analysis, ASE analysis and correlation analysis

From: Genome-wide analysis of expression QTL (eQTL) and allele-specific expression (ASE) in pig muscle identifies candidate genes for meat quality traits

Gene_name eQTL analysis ASE analysis Correlation analysis
SNP_id Fdr SNP_id Num_Het Num_ASE Ratio Traits Cor Fdr
HUS1 18:48910892 2.39E − 19 18:48526014 122 71 0.58 mean_B −0.27 2.82E − 02
mean_H −0.30 4.03E − 02
SPECC1 12:59392739 3.75E − 14 12:59557437 120 26 0.22 pH_24h 0.25 3.18E − 02
mean_B −0.24 4.84E − 02
METTL22 3:34053010 1.99E − 11 3:34040204 78 25 0.32 mean_H −0.29 4.49E − 02
ZFAND2B 15:120963216 4.85E − 06 15:121243305 74 73 0.99 pH_45min −0.33 1.97E − 03
PYGM 2:7381573 1.19E − 04 2:7407552 109 102 0.94 pH_45min 0.35 6.92E − 04
mean_B 0.28 2.73E − 02
ENSSSCG00000009631 14:7718361 4.29E − 04 14:6978183 160 50 0.47 pH_24h −0.25 3.01E − 02
ABRA 4:30027414 4.36E − 04 4:30712640 108 107 0.99 mean_B −0.28 2.59E − 02
RSL1D1 3:30749727 2.59E − 03 3:31285647 117 16 0.14 pH_24h 0.29 1.05E − 02
CAV3 13:64696229 3.04E − 03 13:65131086 122 97 0.80 pH_24h −0.25 3.16E − 02
mean_L 0.32 2.79E − 02
GMPR 7:12312194 3.07E − 03 7:12261459 126 124 0.98 pH_24h −0.25 2.93E − 02
NTN4 5:86726806 3.83E − 03 5:87783446 89 11 0.12 mean_L −0.36 6.25E − 03
GPC1 15:139006307 5.29E − 03 15:139483525 119 56 0.47 pH_45min −0.26 4.99E − 02
TRIM54 3:111962587 7.51E − 03 3:111836687 108 36 0.33 mean_B −0.26 4.08E − 02
pH_24h 0.26 2.83E − 02
LGMN 7:114180118 8.75E − 03 7:114200066 145 40 0.28 pH_45min −0.28 2.33E − 02
CACNA1S 10:23528382 1.14E − 02 10:23530021 133 71 0.53 pH_45min 0.26 4.43E − 02
ENSSSCG00000020808 3:16083309 1.59E − 02 3:16844732 109 41 0.38 mean_B −0.27 2.73E − 02
MTRR 16:74265935 1.81E − 02 16:74245560 66 13 0.20 pH_24h 0.24 4.53E − 02
CCT8 13:192188992 1.83E − 02 13:192414026 58 12 0.21 mean_B −0.27 2.96E − 02
ZFAND2A 3:930630 2.11E − 02 3:757286 106 21 0.20 pH_24h 0.25 3.18E − 02
RRP7A 5:6407132 2.17E − 02 5:6216045 137 44 0.32 mean_B −0.28 2.73E − 02
SOD2 1:7722553 2.27E − 02 1:7679607 184 115 0.63 pH_24h 0.25 3.03E − 02
ANKRD10 11:78298873 2.37E − 02 11:77325740 94 10 0.11 pH_24h 0.24 4.35E − 02
SDR39U1 7:75705436 2.64E − 02 7:74851797 99 45 0.45 mean_B 0.24 4.84E − 02
PLA2G7 7:41182729 3.35E − 02 7:41498072 186 49 0.26 mean_B −0.27 2.73E − 02
NAT9 12:5991040 3.53E − 02 12:6466570 131 53 0.40 mean_H −0.30 4.03E − 02
NPNT 8:116112745 3.72E − 02 8:115860561 44 15 0.34 pH_24h 0.26 2.55E − 02
GRK3 14:44316076 3.76E − 02 14:43439845 68 33 0.49 pH_24h 0.25 3.33E − 02
SMIM3 2:150955856 3.95E − 02 2:151763489 121 11 0.09 mean_B −0.25 4.48E − 02
ACTN3 2:6263381 4.35E − 02 2:5861691 117 109 0.93 pH_24h −0.27 2.00E − 02
NR4A1 5:17110306 4.74E − 02 5:17405098 74 22 0.30 pH_45min 0.49 1.86E − 09
CTGF 1:31914264 4.75E − 02 1:31676377 96 18 0.19 pH_45min 0.27 2.77E − 02
DYNLT1 1:8669156 4.82E − 02 1:8562162 129 58 0.45 pH_24h −0.30 8.57E − 03
KLHL40 13:27052606 4.90E − 02 13:26209704 86 33 0.38 pH_24h 0.30 9.62E − 03
  1. Num_Het” represents the total number of observed heterozygotes, and “Num_ASE” means the number of heterozygotes that displayed ASE
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