Table 3.
Biological candidate genes at novel loci
| Locus | Trait | Lead SNP | Chr | Position | Nearest Gene | Nearest Gene (kb) | Number of Genes within 100 kb | Literature Candidate | Nonsynonymous Variants (r2>0.8) | eQTL Gene (P<5×10−8) | Other Trait Associations of Similar Effect Direction(P < 0.05) |
|---|---|---|---|---|---|---|---|---|---|---|---|
| PDGFC | HDL-C | rs6822892 | 4 | 157,734,675 | PDGFC | 0.0 | 1 | PDGFC | FI*, HOMA-IR, 2hr G, 2hr I, T2D | ||
| CCND3-TAF8 | HDL-C | rs4714556 | 6 | 41,993,229 | CCND3 | 0.0 | 4 | 2hr I | |||
| NCOA2 | HDL-C | rs10504476 | 8 | 71,267,629 | NCOA2 | 0.0 | 1 | NCOA2 | |||
| SNTB1 | HDL-C | rs4871137 | 8 | 121,868,551 | SNTB1 | 44.2 | 1 | SNTB1 | FG, 2hr G, WHR* | ||
| CD163-APOBEC1 | HDL-C | rs10743940 | 12 | 7,651,138 | CD163 | 0.0 | 3 | APOBEC1 | CD163 (I342V) | ||
| CD163-APOBEC1 | HDL-C | rs1419980 | 12 | 7,774,892 | APOBEC1 | 27.1 | 3 | APOBEC1 | |||
| NID2-PTGDR | HDL-C | rs10144765 | 14 | 52,559,930 | NID2 | 24.1 | 2 | PTGDR, PTGER2 | |||
| TRAM2 | LDL-C, TC | rs2239620 | 6 | 52,452,585 | TRAM2-AS1 | 3.8 | 4 | ||||
| THOP1 | TC | rs941408 | 19 | 2,814,181 | THOP1 | 0.5 | 8 | S1PR4 | HOMA-B, SCC, UACR | ||
| WDR11-FGFR2 | TG | rs10886863 | 10 | 122,929,493 | WDR11 | 263.1 | 0 | FGFR2 | Adiponectin*, CAD | ||
| GPR180 | TG | rs1341267 | 13 | 95,284,980 | GPR180 | 1.9 | 5 | GPR180 | SBP | ||
| ADPGK | TG | rs8027181 | 15 | 73,088,869 | ADPGK-AS1 | 0.0 | 3 | BBS4 | BBS4 (I182T) | BMI*, FI*, HOMA-B, WHR | |
| BPTF | TG | rs12602912 | 17 | 65,870,073 | BPTF | 0.0 | 1 | PITPNC1 | BPTF | BMI*, HbA1c, T2D |
Biological candidate genes at each of the novel lipid loci identified in the East Asian and trans-ancestry meta-analyses. For loci associated with more than one trait, the lead variant was selected based on the trait with the smallest P-value. For loci detected in both East Asian and trans-ancestry analyses, the lead variant was selected from the East Asian meta-analysis results. Annotation of nearest gene and number of nearby genes were obtained from UCSC Genome Browser. Literature candidates were selected after manual investigation of genes within 100 kb of the index variant for biological relevance to lipids. Detailed decription of literature candidates and references can be found in Supplementary Text. eQTLs were identified in METSIM subcutaneous adipose (see methods). Detailed information about the METSIM eQTL results can be found in Supplementary Table 10. Detailed information about the other trait associations can be found in Supplementary Table 13. Physical positions based on hg19. For "Other Trait Associations", asterisks (*) indicate other traits that met a multiple testing threshold of 0.0033 (15 variants).
CAD, coronary artery disease; DBP, distolic blood pressure; FG, fasting glucose; FI, fasting insulin; G, glucose; I, insulin; MA, microalbuminuria; SBP, systolic blood pressure; SC, serum creatinine; SCC, serum cystatin C T2D, type 2 diabetes; UACR, urinary albumin-creatinine ratio; WHR, waist-hip ratio.