Table 2.
Top Association Results for Low-Frequency Variants Based on Level of Statistical Significance
| Gene | dbSNP ID | Mutation (Substitution) | Chr: Positiona | MAFb | Betac | p Value |
|---|---|---|---|---|---|---|
| HDL-C – EA (n = 42,208) | ||||||
| ANGPTL4 | rs116843064 | c.118G>A (p.Glu40Lys) | 19: 8,429,323 | 2.01% | 4 mg/dl | 1.7 × 10−29 |
| LIPG | rs77960347 | c.1187A>G (p.Asn396Ser) | 18: 47,109,955 | 1.27% | 5 mg/dl | 5.1 × 10−27 |
| LPL | rs268 | c.953A>G (p.Asn318Ser) | 8: 19,813,529 | 1.78% | −3 mg/dl | 2.4 × 10−19 |
| LDL-C – EA (n = 39,186) | ||||||
| PCSK9 | rs11591147 | c.137G>T (p.Arg46Leu) | 1: 55,505,647 | 1.54% | −17 mg/dl | 2.7 × 10−59 |
| APOB | rs5742904 | c.10580G>A (p.Arg3527Gln) | 2: 21,229,160 | 0.05% | 71 mg/dl | 5.6 × 10−34 |
| CBLC | rs3208856 | c.1075C>T (p.His359Tyr) | 19: 45,296,806 | 3.43% | −8 mg/dl | 6.2 × 10−30 |
| Triglycerides – EA (n = 39,859) | ||||||
| ANGPTL4 | rs116843064 | c.118G>A (p.Glu40Lys) | 19: 8,429,323 | 2.02% | −15% | 2.9 × 10−37 |
| LPL | rs268 | c.953A>G (p.Asn318Ser) | 8: 19,813,529 | 1.76% | 14% | 1.2 × 10−22 |
| MAP1A | rs55707100 | c.7046C>T (p.Pro2349Leu) | 15: 43,820,717 | 3.25% | 9% | 1.4 × 10−17 |
| HDL-C – AA (n = 14,330) | ||||||
| PCSK7 | rs142953140 | c.1511G>A (p.Arg504His) | 11: 117,089,205 | 0.2% | 17 mg/dl | 3.4 × 10−20 |
| CETP | rs34119551 | c.17T>A (p.Val6Asp) | 16: 56,995,908 | 0.24% | 16 mg/dl | 2.0 × 10−19 |
| LCAT | rs35673026 | c.340G>A (p.Val114Met) | 16: 67,976,851 | 0.34% | 10 mg/dl | 2.0 × 10−10 |
| LDL-C – AA (n = 14,227) | ||||||
| PCSK9 | rs28362286 | c.2037C>A (p.Cys679∗) | 1: 55,529,215 | 0.87% | −40 mg/dl | 1.5 × 10−57 |
| PCSK9 | rs67608943 | c.426C>G (p.Tyr142∗) | 1: 55,512,222 | 0.30% | −35 mg/dl | 2.6 × 10−16 |
| APOE | rs769455 | c.487C>T (p.Arg163Cys) | 19: 45,412,040 | 1.93% | −12 mg/dl | 3.6 × 10−12 |
| Triglycerides – AA (n = 14,351) | ||||||
| APOE | rs769455 | c.487C>T (p.Arg163Cys) | 19: 45,412,040 | 1.93% | 21% | 2.3 × 10−18 |
| COL18A1 | rs114139997 | c.331G>A (p.Gly111Arg) | 21: 46,875,775 | 1.93% | −16% | 1.6 × 10−11 |
| ZNF259 | rs35120633 | c.791C>T (p.Ala264Val) | 11: 116,655,600 | 2.96% | 13% | 2.7 × 10−12 |
Results are based on 42,208 European ancestry (EA) individuals and 14,330 African ancestry (AA) individuals.
a
Chr: Position is reported in UCSC Genome Browser build hg19.
b
MAF, minor allele frequency.
c
Beta is based on the geometric mean for triglycerides.