Table 4 List of genes that are differentially expressed and that co-localize with dairy QTL
From: Analyzing the genomic and transcriptomic architecture of milk traits in Murciano-Granadina goats
QTL | Leading SNP | Chromosome | Start | End | Gene symbol | T1 vs. T2 | T1 vs. T3 | T2 vs. T3 | |||
|---|---|---|---|---|---|---|---|---|---|---|---|
log2FC | q-value | log2FC | q-value | log2FC | q-value | ||||||
1 | rs268253425 | 2 | 130,227,819 | 130,232,923 | MSTN | – | – | −2.17 | 3.30E-05 | −1.66 | 1.14E-05 |
2 | rs268258472 | 3 | 113,070,996 | 113,098,602 | SH2D1B | – | – | 1.53 | 3.42E-04 | – | – |
3 | 113,497,530 | 113,528,836 | HSD17B7 | – | – | −2.18 | 1.87E-09 | − 2.08 | 5.91E-13 | ||
3 | 113,589,998 | 113,598,576 | CCDC190 | – | – | 2.15 | 3.31E-02 | – | – | ||
3 | 113,876,670 | 113,883,784 | RGS4 | – | – | −3.45 | 1.10E-03 | −3.25 | 1.73E-04 | ||
4 | rs268251267 | 6 | 15,922,309 | 15,965,996 | CFI | – | – | 2.20 | 4.46E-04 | 2.33 | 1.08E-05 |
6 | rs268268356, rs268290907 | 6 | 84,458,894 | 84,563,377 | LOC102185449 | – | – | – | – | −2.04 | 2.62E-02 |
6 | 84,667,577 | 84,721,849 | LOC102186288 | – | – | −4.57 | 7.95E-08 | −3.96 | 5.03E-10 | ||
6 | 85,137,434 | 85,152,951 | LOC102172432 | – | – | – | – | − 3.91 | 3.79E-03 | ||
6 | 85,878,003 | 85,901,026 | LOC102169846 | – | – | −6.10 | 4.46E-07 | −6.24 | 6.03E-06 | ||
6 | 85,978,463 | 85,995,270 | CSN1S1 | – | – | −8.17 | 1.31E-28 | −8.03 | 8.28E-28 | ||
6 | 86,006,250 | 86,015,321 | CSN2 | – | – | −7.24 | 5.06E-15 | −7.23 | 9.68E-15 | ||
6 | 86,076,845 | 86,093,539 | CSN1S2 | – | – | −8.00 | 1.83E-18 | −8.18 | 1.50E-19 | ||
6 | 86,093,738 | 86,115,903 | LOC102178810 | – | – | −6.50 | 4.36E-12 | −5.91 | 2.77E-11 | ||
6 | 86,197,263 | 86,211,376 | CSN3 | – | – | −5.16 | 2.76E-11 | −5.12 | 4.67E-11 | ||
6 | 86,427,932 | 86,443,025 | AMTN | 1.94 | 2.72E-02 | −2.59 | 4.31E-06 | −4.56 | 4.61E-12 | ||
7 | rs268250457 | 11 | 71,885,505 | 71,909,335 | GCKR | – | – | −1.96 | 5.40E-09 | – | – |
11 | 72,204,731 | 72,208,863 | TCF23 | – | – | 2.04 | 3.56E-03 | 1.56 | 2.26E-02 | ||
11 | 72,818,025 | 72,863,960 | DRC1 | – | – | 2.55 | 2.54E-07 | 1.71 | 6.22E-04 | ||
8 | rs268256521 | 12 | 67,360,683 | 67,392,416 | EBPL | – | – | −2.05 | 6.24E-13 | −2.32 | 7.71E-12 |
12 | 68,130,994 | 68,150,636 | CYSLTR2 | – | – | 1.57 | 1.43E-06 | – | – | ||
9 | rs268236131 | 13 | 53,376,787 | 53,378,322 | TNFRSF6B | – | – | 1.64 | 6.44E-04 | – | – |
13 | 53,475,687 | 53,483,660 | EEF1A2 | – | – | 2.07 | 2.39E-02 | – | – | ||
13 | 53,771,553 | 53,785,372 | SLC17A9 | – | – | – | – | −1.94 | 5.05E-10 | ||
13 | 54,495,442 | 54,974,847 | CDH4 | – | – | 1.55 | 1.19E-08 | – | – | ||
11 | rs268255959 | 14 | 45,768,357 | 46,228,322 | KCNB2 | – | – | – | – | −1.63 | 1.45E-02 |
14 | 46,685,533 | 46,688,514 | MSC | – | – | 1.58 | 4.90E-07 | – | – | ||
13 | rs268290053 | 15 | 34,071,717 | 34,073,359 | LOC102175876 | 4.50 | 3.70E-04 | −4.06 | 9.75E-04 | −8.56 | 7.66E-10 |
15 | 34,118,282 | 34,119,849 | HBBC | – | – | – | – | −3.72 | 6.30E-04 | ||
14 | rs268266747 | 15 | 63,018,327 | 63,025,893 | C15H11orf87 | – | – | 4.01 | 7.24E-05 | – | – |
15 | rs268236985 | 16 | 39,165,138 | 39,176,197 | TNFSF18 | – | – | 1.71 | 1.23E-02 | – | – |
16 | 40,049,635 | 40,096,376 | TNFRSF8 | – | – | 1.53 | 5.39E-04 | – | – | ||
16 | rs268253363 | 16 | 47,058,035 | 47,175,045 | AJAP1 | – | – | 2.42 | 2.31E-09 | 1.74 | 3.18E-05 |
16 | 47,851,111 | 47,857,057 | SMIM1 | – | – | −1.53 | 3.69E-14 | −1.52 | 2.29E-15 | ||
16 | 47,858,258 | 47,874,280 | CCDC27 | – | – | −1.82 | 4.42E-03 | – | – | ||
16 | 48,000,776 | 48,022,801 | LOC102183348 | – | – | 1.70 | 1.01E-03 | – | – | ||
21 | rs268243170 | 23 | 7,662,629 | 7,687,922 | CD83 | – | – | 1.58 | 1.78E-06 | – | – |
22 | rs268240589 | 24 | 49,397,175 | 49,422,345 | LIPG | – | – | −4.10 | 7.56E-11 | −4.25 | 1.14E-11 |
24 | 50,316,631 | 50,490,273 | MAPK4 | – | – | −3.40 | 3.72E-15 | −2.71 | 2.17E-12 | ||