Table 2. Trait-associated SNPs converge on the same downstream genes.
| Complex Trait | Unlinked SNP-pair | Explained trait variance | SNP-pair convergences | eQTL significance | Explained expression variance | ||||
| SNP 1 | SNP 2 | SNP 1 | SNP 2 | on gene (probes) | SNP 1 | SNP 2 | SNP 1 | SNP 2 | |
| Beta thalassemia | rs766432 | rs2071348 | 3.3% [40] | 3.0% [40] | HBG2 a (4010040, 450537, H8v2-6400079) | 2.12×10−29, 7.67×10−37, 6.95×10−07 | 4.22×10−24, 6.46×10−24, 3.80×10−06 | 9.7%, 10.4%, 10.3% | 8.0%, 6.7%, 9.0% |
| rs9376092 | rs766432 | 10.5% [40] | 3.3% [40] | HBG2 a (4010040, 450537) | 1.73×10−32, 9.49×10−39 | 2.12×10−29, 7.67×10−37 | 10.8%, 11.1% | 9.7%, 10.4% | |
| rs9376092 | rs2071348 | 10.5% [40] | 3.0% [40] | HBG2 a (4010040, 450537) | 1.73×10−32, 9.49×10−39 | 4.22×10−24, 6.46×10−24 | 10.8%, 11.1% | 8.0%, 6.7% | |
| F-cell distribution | rs1427407 | rs9399137 | 13.1% [38] | 15.8% [38] | HBG2 a (4010040, 450537) | 1.18×10−28, 1.21×10−36 | 1.70×10−26, 1.86×10−30 | 9.51%, 10.35% | 8.74%, 8.75% |
| Systolic blood pressure | rs3184504 | rs2681492 | N/A | N/A | LOC338758 (6650035) | 1.28×10−06 | 9.17×10−08 | 1.87% | 2.27% |
| Diastolic blood pressure | rs3184504 | rs2681472 | N/A | N/A | LOC338758 (6650035) | 1.28×10−06 | 2.23×10−08 | 1.87% | 2.49% |
| rs653178 | rs2681472 | N/A | N/A | LOC338758 (6650035) | 1.54×10−06 | 2.23×10−08 | 1.85% | 2.49% | |
| Mean corpuscular volume | rs12718597 | rs643381 | 0.26% [41] | 0.50% [41] | VWCE (1450608) | 3.39×10−10 | 1.74×10−06 | 2.65% | 1.61% |
| rs2540917 | rs643381 | 0.24% [41] | 0.50% [41] | ESPN (3440630) | 1.95×10−15 | 6.20×10−07 | 4.99% | 1.99% | |
| rs4895441 | rs2540917 | 1.12% [41] | 0.24% [41] | HBG2 a (4010040, 450537) | 2.74×10−32, 1.31×10−38 | 2.87×10−19, 3.19×10−18 | 10.71%, 10.99% | 6.32%, 5.29% | |
| rs4895441 | rs643381 | 1.12% [41] | 0.50% [41] | RAP1GAP a (4890181) | 2.46×10−06 | 5.57×10−06 | 1.51% | 1.41% | |
| PDZK1IP1 (3170270) | 4.27×10−06 | 7.44×10−10 | 1.45% | 2.55% | |||||
| Mean corpuscular hemoglobin | rs628751 | rs7776054 | 0.34% [41] | 1.02% [41] | PDZK1IP1 (3170270) | 7.74×10−10 | 8.97×10−07 | 2.55% | 1.65% |
| Mean platelet volume | rs12485738 | rs11602954 | 0.93% [42] | 0.41% [42] | GP9 b (1050292) | 3.62×10−17 | 1.14×10−07 | 4.82% | 1.93% |
| GNG11 (1580025) | 9.67×10−12 | 2.23×10−06 | 3.22% | 1.52% | |||||
| F13A1 (2230241) | 5.37×10−09 | 3.13×10−09 | 2.54% | 2.38% | |||||
| SAMD14 b (5560280) | 4.08×10−18 | 3.10×10−06 | 5.05% | 1.47% | |||||
| C19orf33 (630470) | 6.26×10−11 | 1.16×10−08 | 2.86% | 2.37% | |||||
| VCL b (70592) | 7.49×10−07 | 6.81×10−06 | 1.72% | 1.39% | |||||
| rs12485738 | rs11071720 | 0.93% [42] | 0.18% [42] | TPM1 (5560246, 610519) | 1.47×10−08, 1.45×10−06 | 1.38×10−13, 4.41×10−13 | 2.58%, 1.60% | 4.32%, 3.58% | |
| Multiple sclerosis | rs2523393 | rs9271366 | N/A | N/A | TGFBR2 (2340324) | 5.15×10−07 | 1.07×10−06 | 2.01% | 1.90% |
| Type 1 diabetes | rs9272346 | rs11171739 | N/A | N/A | KRT18 (6580270) | 1.87×10−06 | 4.72×10−06 | 2.06% | 1.70% |
| rs9272346 | rs1701704 | N/A | N/A | KRT18 (6580270) | 1.87×10−06 | 9.40×10−06 | 2.06% | 1.39% | |
| Height | rs910316 | rs10946808 | N/A | N/A | BTN3A2 (4610674) | 5.42×10−06 | 9.79×10−10 | 1.40% | 2.60% |
Indicated are 18 pairs of unlinked SNPs that are associated with the same complex phenotype and that also affect the expression levels of the same downstream gene(s) in cis (FDR 0.05) or trans (FDR 0.50).
a Erythrocyte specific gene according to HaemAtlas [43].
b Megakaryocyte specific gene according to HaemAtlas [43].
Explained phenotypic variation is shown for traits when reported in the original papers (indicated in superscript) that describe these SNP – phenotype association.