Trait | SSC | Lead GWAS SNP | seqSNP | ||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
Position (bp) | Line | r2 | Dist (Mb) | pCADD score | VEP | Position (bp) | Open chromatin | Gene | Supporting evidence | ||
LDP | 1 | 158,355,905 | A | 0.84 | − 3.51 | 24.86 | missense | 161,864,397 | No | ENSSSCG00000004911 | - |
LDP | 1 | 160,347,188 | B | 0.97 | − 0.43 | 34.19 | missense | 160,773,437 | No | MC4R | Associated with growth and fatness [2] |
LDP | 1 | 270,354,493 | D | 0.96 | − 0.05 | 30.69 | missense | 270,408,730 | Yes | HMCN2 | Differential methylation between Chinese and YP [27] |
LDP | 2 | 404,057 | B | 0.95 | − 0.03 | 22.4 | missense | 432,824 | Yes | TMEM80 | – |
LDX | 2 | 2,051,230 | D | 0.81 | 0 | 20.4 | missense | 2,048,612 | Yes | SLC22A18 | Hypermethylated in Duroc (fat), compared to Pietrain (lean) pigs [28] |
LDP | 2 | 2,215,904 | B | 0.91 | 0 | 11.74 | intron | 2,213,982 | No | OSBPL5 | Candidate gene for ADG [29] |
LDP | 5 | 66,103,958 | D | 0.98 | − 0.01 | 13.49 | intron | 66,109,890 | Yes | CCND2 | Overexpressed in SM muscle [30] |
LDX | 5 | 66,103,958 | D | 0.98 | − 0.01 | 13.49 | intron | 66,109,890 | Yes | CCND2 | Overexpressed in SM muscle [30] |
LDP | 6 | 45,744,000 | A | 0.86 | − 6.29 | 34.95 | missense | 52,032,079 | Yes | GIPR | – |
LDX | 7 | 20,586,603 | D | 0.91 | 0.28 | 9.91 | intron | 20,305,193 | No | CARMIL1 | Suggested gene for backfat GWAS [31] |
LDP | 7 | 30,095,798 | D | 0.94 | − 0.08 | 14.82 | missense | 30,179,826 | Yes | GRM4 | eQTL for fatty acid composition [32] |
LDX | 7 | 30,095,798 | D | 0.94 | − 0.08 | 14.82 | missense | 30,179,826 | Yes | GRM4 | eQTL for fatty acid composition [32] |
LDP | 7 | 30,317,219 | A | 0.88 | − 2.11 | 28.78 | synonymous | 32,427,677 | No | CPNE5 | Candidate gene for muscle lightness [33] |
LDP | 7 | 30,317,219 | B | 0.87 | − 0.03 | 17.58 | 3 prime UTR | 30,350,337 | Yes | NUDT3 | |
LDP | 9 | 47,650,875 | A | 0.96 | 0.18 | 11.79 | intron | 47,475,749 | Yes | ARHGEF12 | Â |
LDX | 9 | 47,650,875 | D | 0.92 | 0.24 | 7.22 | intron | 47,406,822 | No | POU2F3 | – |
LDP | 12 | 25,532,133 | A | 0.93 | 0.23 | 34.62 | missense | 25,299,992 | No | ENSSSCG00000030269 | – |
LDP | 16 | 33,283,559 | B | 0.92 | 0.09 | 17.4 | intron | 33,194,036 | No | ARL15 | Candidate gene for growth [36] |
LDP | 16 | 34,100,484 | C | 0.96 | 0.05 | 43.19 | missense | 34,048,944 | No | ENSSSCG00000016898 | – |
LDX | 16 | 34,893,593 | C | 0.9 | 0.84 | 43.19 | missense | 34,048,944 | No | ENSSSCG00000016898 | – |
LDP | 16 | 48,157,349 | C | 0.84 | − 3.7 | 21.66 | synonymous | 51,852,935 | Yes | SH3PXD2B | Implicated in growth rate of pigs [37] |
LDP | 17 | 5,307,502 | C | 0.91 | 0.06 | 34.21 | synonymous | 5,246,513 | Yes | SLC7A2 | – |
LDX | 17 | 5,307,502 | C | 0.91 | 0.06 | 34.21 | synonymous | 5,246,513 | Yes | SLC7A2 | – |
LDP | 18 | 2,380,106 | A | 0.91 | − 0.04 | 23.47 | intergenic | 2,422,486 | No | ENSSSCG00000042976 | – |
PHLOIN | 15 | 120,437,865 | D | 0.97 | − 0.28 | 41.82 | synonymous | 120,713,562 | Yes | RNF25 | Suggested role in muscle development in cattle [38] |