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. 2020 Oct 28;10:18434. doi: 10.1038/s41598-020-75612-6

Table 2.

Genome-wide and suggestively significant GWAS results.

Pheno-type Chr Lead-SNP BP MAF P B SE Genomic region Candidate gene Position of functional candidate gene Functional link Region in strong LD with lead-SNP, r2 > 0.8
LDL-C 2 82,111,387 0.10 4.60E−07  − 6.78 1.34 Intron, FCHO2 FCHO2 82,117,891-82,248,407 The FCHO2 gene product is involved in clathrin-mediated endocytosis of LDL-C31 81,958,868-82,859,296
Csta 3 15,599,531 0.08 7.30E−07  − 4.24 0.86 Intron, CALN1 n/a n/a 15,580,136-15,637,077
Des 6 157,486,305 0.19 1.06E−11  − 13.58 2.00 Intron, DHCR24 DHCR24 157,483,794-157,519,059 DHCR24 encodes the enzyme that converts desmosterol to cholesterol32,33 157,481,935-157,486,331
Sint 7 57,828,885 0.22 3.62E−07 18.54 3.64 Intron, LINGO1 n/a n/a 57,707,845-60,000,893
Bsit 13 53,636,117 0.39 2.57E−07  − 41.50 8.05 Intergenic n/a n/a 53,062,778-54,254,135
Sphy 13 75,586,650 0.32 1.30E−08  − 106.55 18.74 Intergenic n/a n/a 75,586,650-75,723,225
Cste 13 79,228,431 0.47 2.58E−07  − 65.28 12.67 Intergenic

FAIM

FOXL2

 79,398,049-79,411,772 79,708,693-79,709,825 FAIM deficiency enhances SREBP signaling and promotes lipogenesis in liver34. FOXL2 represses expression of Star, which controls cholesterol transport in mitochondria35,36 79,109,893-79,247,374
Sint 13 88,500,932 0.53 2.37E−07 15.30 2.96 Intergenic CP 89,398,185-89,463,223 CP encodes ceruloplasmin. Ceruloplasmin concentrations are correlated with serum triglyceride and cholesterol levels37 88,087,429-89,821,031
Lat 13 88,852,202 0.50 3.38E−07 8.02 1.57 Intergenic CP 89,398,185-89,463,223 Do 88,084,836-90,249,783
Des 13 89,367,223 0.48 4.67E−07 8.48 1.68 Intron, HPS3 CP 89,398,185-89,463,223 Do 88,084,836-91,010,648
TC 13 89,563,053 0.47 2.84E−07 4.65 0.91 Intergenic CP 89,398,185-89,463,223 Do 88,084,836-89,993,057
Lan 15 127,265,666 0.20 8.43E−08 0.57 0.11 Intron, NYAP2 n/a 127,032,688-127,295,095 n/a 127,263,233-127,267,733

Summary data of lead-SNPs surpassing the genome-wide (p < 4.8E−08) or suggestive (p < 4.8E−07) significance level. Results are listed in chromosomal and positional order. Chromosome number (Chr) and base-pair (BP) position refer to pig genome assembly Sscrofa 11.1. MAF = minor allele frequency. P = p value. B = regression coefficient. SE = standard error for B. r2 = The squared correlation coefficient between pairs of SNPs as a measure for linkage disequilibrium (LD). Phenotype abbreviations: Serum levels of the following lipids, Lanosterol (Lan), Lathosterol (Lat), Desmosterol (Des), Sum of intermediates in the cholesterol synthesis pathway (Sint) i.e. Lan + Lat + Des, Betasitosterol (Bsit), Campesterol (Cste), Stigmasterol (Stig) Sum of phytosterols (Sphy) i.e. Bsit + Cste + Stig, Coprostanol (Csta), low-density lipoprotein cholesterol (LDL-C), total cholesterol (TC).