Table 2 |. 2-kb sliding 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 STAAR-O P < 1.88 × 10−8; conditional STAAR-O P < 3.57 × 10−4) using discovery samples are presented in the table. The unconditional significant threshold was defined by the multiple comparisons using the Bonferroni correction (0.05/(2.66 × 106) = 1.88 × 10−8). STAAR-O is a two-sided test. Chr (Chromosome); Start Location (Start location of the 2kb sliding window); End Location (End location of the 2-kb sliding window); #SNV (Number of rare variants (MAF < 1%) in the 2-kb sliding window; STAAR-O (STAAR-O 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); n/a, no variant adjusted in the conditional analysis. Physical positions of each window are on build hg38.
| Trait | Chr | Start Location | End Location | Gene | Discovery |
Replication |
Variants Adjusted | ||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| #SNV | STAAR-O (Unconditional) | STAAR-O (Conditional) | #SNV | STAAR-O (Unconditional) | STAAR-O (Conditional) | ||||||
| HDL-C | 8 | 57,071,644 | 57,073,643 | Intergenic (IMPAD1) | 111 | 1.79E-08 | 1.79E-08 | 53 | 8.38E-01 | 8.38E-01 | n/a |
| 11 | 116,802,930 | 116,804,929 | Intergenic (ZPR1) | 135 | 1.25E-08 | 4.31E-08 | 76 | 9.49E-05 | 2.02E-04 | rs964184, rs12269901 | |
| 11 | 117,146,930 | 117,148,929 | Intronic (PAFAH1B2) | 165 | 5.98E-09 | 8.28E-08 | 98 | 6.02E-04 | 1.12E-03 | rs964184, rs12269901 | |
| 11 | 117,147,930 | 117,149,929 | Intronic (PAFAH1B2) | 168 | 8.85E-09 | 1.22E-07 | 96 | 8.72E-04 | 1.64E-03 | rs964184, rs12269901 | |
| 16 | 56,760,029 | 56,762,028 | Intronic (NUP93) | 132 | 1.38E-08 | 9.65E-06 | 68 | 2.45E-01 | 1.15E-01 | rs247616, rs5883, rs7499892, rs17231520, rs5880 | |
| 16 | 56,761,029 | 56,763,028 | Intronic (NUP93) | 141 | 1.50E-08 | 1.09E-05 | 73 | 5.87E-01 | 2.26E-01 | rs247616, rs5883, rs7499892, rs17231520, rs5880 | |
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| LDL-C | 1 | 55,333,498 | 55,335,497 | Intergenic (GOT2P1) | 171 | 6.66E-16 | 5.81E-07 | 95 | 1.27E-06 | 5.81E-07 | rs11591147, rs28362263, rs505151, rs12117661, rs472495 |
| 1 | 55,334,498 | 55,336,497 | Intergenic (GOT2P1) | 148 | 5.55E-16 | 5.49E-07 | 81 | 1.20E-06 | 5.49E-07 | rs11591147, rs28362263, rs505151, rs12117661, rs472495 | |
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| TG | 11 | 117,146,930 | 117,148,929 | Intronic (PAFAH1B2) | 164 | 7.81E-19 | 4.13E-18 | 93 | 2.17E-17 | 5.66E-17 | rs964184, rs9804646, rs3135506, rs2266788 |
| 11 | 117,147,930 | 117,149,929 | Intronic (PAFAH1B2) | 165 | 1.15E-18 | 6.11E-18 | 94 | 3.47E-17 | 9.13E-17 | rs964184, rs9804646, rs3135506, rs2266788 | |
| 19 | 44,882,528 | 44,884,527 | Intronic (NECTIN2) | 145 | 1.06E-08 | 2.18E-07 | 88 | 2.71E-02 | 8.07E-01 | rs12721054, rs5112, rs429358 | |
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| TC | 1 | 55,333,498 | 55,335,497 | Intergenic (GOT2P1) | 175 | 1.98E-13 | 3.83E-14 | 101 | 5.84E-07 | 1.88E-07 | rs11591147, rs28362263, rs505151, rs12117661, rs2495477 |
| 1 | 55,334,498 | 55,336,497 | Intergenic (GOT2P1) | 149 | 1.80E-13 | 3.49E-14 | 90 | 5.53E-07 | 1.78E-07 | rs11591147, rs28362263, rs505151, rs12117661, rs2495477 | |
| 19 | 44,894,528 | 44,896,527 | Intronic (TOMM40) | 180 | 2.73E-10 | 8.95E-08 | 97 | 2.68E-03 | 4.22E-01 | rs7412, rs429358, rs12721054 | |