Table 2.
26 pleiotropic genomic loci identified by FUMA using PLACO results
| Trait pair | Top SNP | Locus boundary | Region | Nearest gene | PP.H3 | PP.H4 | Best causal SNP | SNP.PP.H4 |
|---|---|---|---|---|---|---|---|---|
| PCOS-BCALL | rs10423928 | 19:46,179,043–46202172 | 19q13.32 | GIPR | 2.53E-01 | 2.28E-02 | rs4849879 | 1.40E-01 |
| PCOS-BCALL | rs11012730 | 10:21,766,969–22,275,118 | 10p12.31 | SKIDA1 | 1.99E-01 | 1.63E-02 | rs552647 | 1.24E-01 |
| PCOS-BCALL | rs147872430 | 5:44,992,980–45933347 | 5p12 | NA | 4.53E-02 | 2.14E-02 | rs930395 | 7.44E-01 |
| PCOS-BCALL | rs17630711 | 3:27,421,024–27553889 | 3p24.1 | SLC4A7 | 2.91E-01 | 2.43E-02 | rs60954078 | 2.13E-01 |
| PCOS-BCALL | rs2926589 | 8:76,362,101–76689287 | 8q21.13 | HNF4G | 1.93E-01 | 5.37E-02 | rs72658071 | 4.03E-01 |
| PCOS-BCALL | rs45577136 | 16:52,566,220–52630972 | 16q12.1 | TOX3 | 8.82E-02 | 1.22E-01 | rs12251016 | 2.07E-01 |
| PCOS-BCALL | rs4980554 | 11:69,281,227–69,285,786 | 11q13.3 | NA | 2.00E-01 | 1.35E-02 | rs719338 | 2.76E-01 |
| PCOS-BCALL | rs61874140 | 10:123,435,982–123,435,982 | 10q26.13 | NA | 1.33E-01 | 1.31E-02 | rs2981579 | 8.35E-01 |
| PCOS-BCALL | rs73949122 | 2:121,153,284–121,180,803 | 2q14.2 | NA | 1.39E-01 | 2.37E-02 | rs78540526 | 1.00E + 00 |
| PCOS-BCALL | rs753271 | 10:80,853,575–80869471 | 10q22.3 | ZMIZ1 | 2.41E-01 | 1.97E-02 | rs4784227 | 9.55E-01 |
| PCOS-BCALL | rs8050136 | 16:53,797,908–53845487 | 16q12.2 | FTO | 1.83E-01 | 8.12E-01 | rs62048402 | 2.03E-01 |
| PCOS-BCALL | rs851984 | 6:151,970,639–152052215 | 6q25.1 | ESR1 | 7.87E-02 | 6.43E-01 | rs10423928 | 2.69E-01 |
| PCOS-ERNBC | rs1121980 | 16:53,797,908–53845487 | 16q12.2 | FTO | 2.37E-01 | 7.79E-02 | rs4528762 | 9.99E-01 |
| PCOS-ERNBC | rs1293960 | 6:151,970,639–151970639 | 6q25.1 | NA | 2.83E-01 | 2.43E-02 | rs9397437 | 2.28E-01 |
| PCOS-ERNBC | rs4849857 | 2:120,986,708–121070811 | 2q14.2 | NA | 1.60E-01 | 8.35E-01 | rs55872725 | 9.14E-02 |
| PCOS-ERPBC | rs10423928 | 19:46,179,043–46202172 | 19q13.32 | GIPR | 1.66E-01 | 1.70E-02 | rs490706 | 6.21E-02 |
| PCOS-ERPBC | rs11012730 | 10:21,766,969–22,275,118 | 10p12.31 | SKIDA1 | 1.42E-01 | 3.64E-02 | rs985261 | 3.97E-02 |
| PCOS-ERPBC | rs11706019 | 3:27,421,024–27553889 | 3p24.1 | SLC4A7 | 2.91E-01 | 2.43E-02 | rs60954078 | 3.34E-01 |
| PCOS-ERPBC | rs12380632 | 9:110,891,494–110941095 | 9q31.2 | LOC105376214 | 1.30E-01 | 1.41E-02 | rs7862747 | 2.54E-01 |
| PCOS-ERPBC | rs13131992 | 4:175,819,086–175870676 | 4q34.1 | ADAM29 | 8.71E-02 | 1.32E-01 | rs10828248 | 2.73E-01 |
| PCOS-ERPBC | rs45577136 | 16:52,566,220–52630972 | 16q12.1 | TOX3 | 1.33E-01 | 1.31E-02 | rs2981579 | 7.34E-01 |
| PCOS-ERPBC | rs4980554 | 11:69,281,227–69,285,786 | 11q13.3 | NA | 1.39E-01 | 2.37E-02 | rs78540526 | 1.00E + 00 |
| PCOS-ERPBC | rs61874140 | 10:123,435,982–123,435,982 | 10q26.13 | NA | 2.41E-01 | 1.94E-02 | rs4784227 | 9.93E-01 |
| PCOS-ERPBC | rs715537 | 22:28,625,685–29,257,046 | 22q12.1 | NA | 1.45E-01 | 8.50E-01 | rs62048402 | 1.29E-01 |
| PCOS-ERPBC | rs8050136 | 16:53,797,908–53845487 | 16q12.2 | FTO | 1.05E-01 | 5.24E-01 | rs10423928 | 3.40E-01 |
| PCOS-ERPBC | rs851984 | 6:152,008,780–152024985 | 6q25.1 | ESR1 | 1.84E-01 | 4.62E-02 | rs62237573 | 1.00E + 00 |
PCOS, polycystic ovary syndrome; BC, breast cancer; ERNBC, estrogen receptor-negative breast cancer; ERPBC, estrogen receptor-positive breast cancer; Best causal, the candidate causal single-nucleotide polymorphism (SNP); PP.H3, posterior probability of H3; PP.H4, posterior probability of H4; SNP.PP.H4, posterior probability of the best causal polymorphism. Locus boundary of each pleiotropic genomic risk locus was denoted as “chromosome: start–end” defined by FUMA for the corresponding trait pair. The top SNP in this locus was also identified as a candidate causal SNP