Table 5.
Distribution of positional and functional SNPs in Pantothenate and CoA biosynthesis and PPAR signaling pathways
| CNP | CPG | 3DO | 3UTR | 5UP | 5UTR | COD | INT | NON | INDEL | SIFT DH | SIFT TH | SIFT TL | TFBS | Total* | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Pantothenate and CoA biosynthesis pathway | |||||||||||||||
| COASY | 7 | 2 | 2 | 2 | 4 | 1 | 5 | 9 | 1 | 2 | 1 | 36 | |||
| PPCS | 3 | 1 | 3 | 19 | 22 | 48 | |||||||||
| ENPP3 | 19 | 6 | 1 | 1 | 1 | 24 | 8 | 1 | 61 | ||||||
| ENPP1 | 18 | 3 | 3 | 1 | 15 | 13 | 1 | 54 | |||||||
| DPYD | 23 | 1 | 1 | 1 | 30 | 6 | 62 | ||||||||
| UPB1 | 11 | 11 | 11 | 2 | 35 | ||||||||||
| VNN2 | 7 | 7 | 9 | 4 | 27 | ||||||||||
| BCAT1 | 6 | 1 | 2 | 2 | 1 | 12 | |||||||||
| VNN1 | 1 | 2 | 4 | 7 | |||||||||||
| DPYS | 1 | 1 | 2 | ||||||||||||
| BCAT2 | 1 | 1 | |||||||||||||
| PPAR signaling pathway | |||||||||||||||
| ACSL5 | 8 | 6 | 3 | 2 | 26 | 24 | 1 | 70 | |||||||
| ACOX3 | 16 | 5 | 16 | 6 | 43 | ||||||||||
| ACSL1 | 4 | 2 | 4 | 1 | 2 | 13 | 11 | 37 | |||||||
| APOA2 | 5 | 1 | 8 | 9 | 9 | 1 | 33 | ||||||||
| MMP1 | 5 | 1 | 1 | 2 | 3 | 12 | 1 | 2 | 27 | ||||||
| CYP4A22 | 1 | 1 | 3 | 4 | 12 | 1 | 3 | 25 | |||||||
| CPT2 | 6 | 2 | 3 | 5 | 7 | 23 | |||||||||
| FABP6 | 1 | 6 | 10 | 2 | 19 | ||||||||||
| SLC27A6 | 18 | 18 | |||||||||||||
| UCP1 | 6 | 3 | 5 | 3 | 17 | ||||||||||
| CD36 | 1 | 1 | 6 | 6 | 14 | ||||||||||
| SLC27A1 | 1 | 2 | 8 | 11 | |||||||||||
| CPT2 | 10 | 10 | |||||||||||||
| FABP1 | 2 | 2 | 5 | 9 | |||||||||||
| ACOX2 | 1 | 1 | 1 | 2 | 1 | 6 | |||||||||
| ILK | 2 | 1 | 1 | 1 | 1 | 6 | |||||||||
| PPARA | 2 | 2 | 2 | 6 | |||||||||||
| CYP27A1 | 1 | 2 | 1 | 1 | 1 | 6 | |||||||||
| FABP7 | 1 | 3 | 1 | 1 | 6 | ||||||||||
| SLC27A5 | 1 | 1 | 1 | 1 | 1 | 5 | |||||||||
| SLC27A2 | 2 | 1 | 1 | 4 | |||||||||||
| PCK1 | 1 | 1 | 2 | 4 | |||||||||||
| SORBS1 | 2 | 2 | 4 | ||||||||||||
| ACOX1 | 1 | 1 | 1 | 3 | |||||||||||
| RXRA | 1 | 1 | 1 | 3 | |||||||||||
| PPARD | 3 | 3 | |||||||||||||
| APOA5 | 1 | 1 | 2 | ||||||||||||
| APOA1 | 1 | 1 | 2 | ||||||||||||
| APOC3 | 1 | 1 | 2 | ||||||||||||
| ACOX1 | 1 | 1 |
The number of nominally associated SNPs (P < 0.05) belonging in each category for each of the pathway genes are shown. Four genes in the pantothenate pathway and 39 genes in the PPAR signaling pathway did not contain any nominally associated SNP and were excluded from the table.
CNP, copy number polymorphism; CPG, CpG island region; 3DO, 3′-downstream (5 kb); 3UTR, 3′ untranslated region (3′UTR); 5UP, 5′-upstream (5 kb); 5UTR, 5′ untranslated region (5′UTR); COD, coding region; INT, intronic; NON, noncoding region; INDEL, insertions and deletions; SIFT DH, amino acid substitution (damaging, high confidence); SIFT TH, amino acid substitution (tolerated, high confidence); SIFT TL, amino acid substitution (tolerated, low confidence); TFBS, transcription factor binding sites.
Total (across rows) of functional and positional SNPs for each gene.