Table 2.
Single nucleotide variants (SNVs) and small insertions and deletions (indels) in linkage disequilibrium (r2 ≥ 0.75) with structural variants associated with hematological traits
| Gene(s) | Locus | SV Breakpoints¹ | SV type² | SV allele frequency | SNV/indel; ref>alt | SNV, indel allele frequency | r2 | SNV/indel P-value³ | SNV/indel Effect Estimate³ | SNV/indel Effect Estimate SE³ |
|---|---|---|---|---|---|---|---|---|---|---|
| - | 2p11.2 | 2:88832769-88860930 | DEL | 1.98E-04 | - | - | - | - | - | - |
| RAB7A | 3q21.3 | 3:128694260-128695207 | DUP | 0.085 | 3:128694296; A > T | 0.08 | 0.781 | 5.60E-08 | −0.002 | 0.0004 |
| SRPRB, TF, TOPBP1 | 3q22.1 | 3:133621201-133784900 | DUP | 0.208 | 3:133789620; A > T | 0.295 | 0.819 | 3.70E-32 | 17.697 | 1.499 |
| C3orf36, LINC02000, RAB6B, SLCO2A1, SRPRB, TF | 3q22.1-q22.2 | 3:133786201-134102300 | DUP | 0.272 | 3:133789620; A > T | 0.295 | 0.791 | 3.70E-32 | 17.697 | 1.499 |
| PSORS1C1 | 6p21.33 | 6:31132409-31132465 | DEL | 0.085 | 6:31133806; G/ > A | 0.084 | 0.99 | 3.15E-06 | 0.109 | 0.023 |
| - | 6p21.32 | 6:32591559-32591660 | DEL | 0.264 | 6:32593469; T > C | 0.277 | 0.999 | 1.23E-08 | 0.084 | 0.015 |
| - | 6p21.1 | 6:41897089-41897626 | DEL | 0.183 | 6:41880062: G > A | 0.186 | 1 | 3.74E-18 | −0.18 | 0.021 |
| CCND3 | 6p21.1 | 6:41985574-41988887 | DEL | 0.007 | 6:41984773; T > G | 0.007 | 0.999 | 4.67E-10 | 0.613 | 0.098 |
| - | 6p23.3 | 6:134878573-134878641 | DUP | 0.044 | 6:134870213; A > G | 0.107 | 0.79 | 7.16E-12 | −0.189 | 0.028 |
| - | 9q22.1 | 9:88923551-88924152 | DEL | 0.034 | 9:88921159; C > A | 0.04 | 0.996 | 1.03E-11 | −0.029 | 0.004 |
| ATXN2 | 12q24.12 | 12:111538485-111542205 | DEL | 0.068 | 12:111599646; G, > A | 0.058 | 0.991 | 7.81E-14 | −6.142 | 0.822 |
| ATXN2 | 12q24.12 | 12:111542097-111542205 | INV | 0.062 | 12:111599646; G > A | 0.058 | 0.936 | 7.81E-14 | −6.142 | 0.822 |
| - | 14q32.33 | 14:105863184-105897962 | DEL | 2.24E-04 | - | - | - | - | - | - |
| - | 14q32.33 | 14:105864247-105902650 | DEL | 7.96E-05 | - | - | - | - | - | - |
| HBA1, HBQ1, HBA2 | 16p13.3 | 16:165396-184701 | DEL | 5.95E-05 | 16:199621; AG > A | 0.0004 | 0.848 | 7.16E-13 | −5.894 | 0.821 |
| HBA1, HBA2, HBQ1 | 16p13.3 | 16:172001-177200 | DEL | 0.057 | - | - | - | - | - | - |
| FAM234A | 16p13.3 | 16:246437-249971 | DEL | 0.006 | 16:244752; G, > A | 0.007 | 0.983 | 2.39E-11 | −0.764 | 0.114 |
| CAPN15 | 16p13.3 | 16:550075-550141 | DEL | 0.025 | 16:550141; T > C | 0.089 | 0.857 | 1.08E-20 | −0.333 | 0.036 |
| KCNJ18 | 17p11.2 | 17:21659501-21795800 | DUP | 0.511 | - | - | - | - | - | - |
| - | 18p11.22 | 18:9621931-9622237 | DEL | 0.791 | 18:9621307; T > G | 0.781 | 0.998 | 1.29E-07 | −0.068 | 0.013 |
| TMPRSS6 | 22q12.3 | 22:37067818-37067888 | DUP | 0.347 | 22:37071230; C > T | 0.438 | 0.774 | 1.47E-13 | 0.125 | 0.017 |
¹Structural variant breakpoints predicted by the Parliament2 pipeline.
²Types of structural variant identified: deletions (DEL), duplications (DUP), inversions (INV).
³Single variant association test statistics performed for SNV, indels, performed using the same sample set used for SV analyses and for the same hematological trait(s).
All p-values are derived from two-sided t-tests and are not adjusted for multiple comparisons.