Table 3 |. Dynamic window analysis results of unconditional analysis and analysis conditional on known common and low-frequency variants.
21,015 discovery samples and 9,123 replication samples from the NHLBI Trans-Omics for Precision Medicine (TOPMed) program are considered in the analysis. Results for the conditionally significant sliding windows (unconditional genome-wide error rate GWπΈπ < 0.05; conditional STAAR-S P < 5.56 Γ 10β4) using discovery samples are presented in the table. STAAR-S is a two-sided test. Chr (Chromosome); Start Location (Start location of the dynamic window); End Location (End location of the dynamic window); #SNV (Number of rare variants (MAF < 1%) in the dynamic window; GWER (genome-wide error rate); STAAR-S (STAAR-S P value); HDL-C (High-density lipoprotein cholesterol); LDL-C (Low-density lipoprotein cholesterol); TG (Triglycerides); TC (Total cholesterol); Variants Adjusted (Adjusted variants in conditional analysis). Physical positions of each window are on build hg38.
| Trait | Chr | Start Location | End Location | Gene | Discovery |
Replication |
Variants Adjusted | |||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| #SNV | GWER | STAAR-S (Unconditional) | STAAR-S (Conditional) | #SNV | STAAR-S (Unconditional) | STAAR-S (Conditional) | ||||||
| HDL-C | 11 | 116,866,780 | 116,867,288 | Intronic (SIK3) | 40 | 0.0295 | 2.24E-09 | 8.45E-09 | 19 | 2.22E-05 | 5.46E-05 | rs964184, rs12269901 |
| 11 | 116,928,564 | 116,929,045 | Intronic (SIK3) | 40 | 0.0025 | 1.50E-10 | 4.43E-10 | 18 | 7.81E-04 | 1.06E-03 | rs964184, rs12269901 | |
|
| ||||||||||||
| LDL-C | 1 | 55,335,150 | 55,335,701 | Intergenic (GOT2P1) | 40 | <0.0005 | 8.58E-18 | 7.49E-19 | 21 | 9.29E-07 | 4.80E-07 | rs11591147, rs28362263, rs505151, rs12117661, rs472495 |
| 19 | 11,319,992 | 11,320,870 | Intronic (TSPAN16) | 60 | 0.02 | 1.44E-09 | 3.16E-05 | 41 | 5.04E-01 | 5.10E-01 | rs12151108, rs688, rs6511720 | |
|
| ||||||||||||
| TG | 11 | 117,147,061 | 117,148,086 | Intronic (PAFAH1B2) | 80 | <0.0005 | 5.10E-16 | 8.55E-15 | 41 | 9.48E-19 | 3.44E-18 | rs964184, rs9804646, rs3135506, rs2266788 |
| 11 | 117,182,856 | 117,183,310 | Intronic (SIDT2) | 40 | <0.0005 | 3.96E-12 | 1.08E-11 | 15 | 3.77E-14 | 6.53E-14 | rs964184, rs9804646, rs3135506, rs2266788 | |
| 11 | 117,349,560 | 117,350,171 | Intronic (CEP164) | 50 | 0.013 | 1.08E-09 | 1.26E-09 | 29 | 4.12E-11 | 6.39E-11 | rs964184, rs9804646, rs3135506, rs2266788 | |
|
| ||||||||||||
| TC | 1 | 55,291,905 | 55,293,502 | Intergenic (GOT2P1) | 140 | 0.0055 | 3.17E-10 | 8.77E-05 | 68 | 4.76E-01 | 2.30E-01 | rs11591147, rs28362263, rs505151, rs12117661, rs2495477 |
| 1 | 55,335,119 | 55,335,584 | Intergenic (GOT2P1) | 40 | <0.0005 | 1.63E-15 | 4.44E-16 | 26 | 2.23E-07 | 7.03E-08 | rs11591147, rs28362263, rs505151, rs12117661, rs2495477 | |
| 19 | 11,319,627 | 11,320,925 | Intronic (TSPAN16) | 110 | <0.0005 | 2.95E-12 | 2.32E-05 | 75 | 3.40E-01 | 5.90E-01 | rs73015024, rs688, rs2278426, rs6511720 | |