Table 2 Genome-wide and suggestively significant GWAS results.

From: Inclusion of endophenotypes in a standard GWAS facilitate a detailed mechanistic understanding of genetic elements that control blood lipid levels

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

  1. 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).
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