Table 2 Cross-trait meta-analysis between obesity-related traits and PCOS (P-CPASSOC < 5× 10−8, single trait P value < 1× 10−3)
SNP | CHR | BP | Alleles (E/A) | BETA (SD) | P-trait | P-PCOS | P-CPASSOC | Genomic coordinates | Genes within clumping area | |
|---|---|---|---|---|---|---|---|---|---|---|
trait | PCOS | |||||||||
BMI and PCOS | ||||||||||
 rs10938397 | 4 | 45182527 | A/G | − 0.03 | − 0.10 | 1.66×10−45 | 8.90×10−04 | 1.25× 10−49 | 45068929–45186832 |  |
 rs705696 | 12 | 56480648 | A/G | − 0.02 | 0.13 | 4.36×10−09 | 1.10× 10−04 | 6.39× 10−10 | 56364321–56564811 | CDK2, ERBB3, ESYT1, IKZF4, MYL6, MYL6B, PA2G4, RAB5B, RPL41, RPS26, SMARCC2, SUOX, ZC3H10 |
 rs1569979 | 14 | 29681294 | A/G | 0.02 | 0.12 | 1.56×10−17 | 9.80× 10−04 | 1.58× 10−18 | 29549249–29702590 |  |
 rs10142183 | 14 | 29723729 | C/G | 0.02 | 0.17 | 1.34× 10−12 | 4.00× 10−05 | 8.00× 10−14 | 29662355–29856951 |  |
 rs11672660 | 19 | 46180184 | T/C | − 0.03 | − 0.13 | 5.93×10−31 | 4.70× 10−04 | 1.87× 10−32 | 46172278–46214297 | FBXO46, GIPR, MIR642A, MIR642B, QPCTL, SNRPD2 |
WHR and PCOS | ||||||||||
 rs3767846 | 1 | 214175126 | A/G | 0.02 | 0.13 | 5.69×10−11 | 5.50× 10−04 | 6.19× 10−12 | 214173840–214192133 | PROX1 |
 rs13032835 | 2 | 165748563 | A/T | − 0.02 | − 0.13 | 2.42× 10−18 | 5.00× 10−05 | 3.59× 10−20 | 165668018–165828042 | COBLL1, LOC101929633, SLC38A11 |
 rs188488867 | 2 | 219784256 | T/C | − 0.04 | 0.31 | 9.03×10−08 | 3.00× 10−04 | 1.35× 10−08 | 219755011–219849633 | CDK5R2, FEV, LINC00608, LOC101928537, WNT10A |
 rs7774737 | 6 | 81145901 | C/G | − 0.04 | − 0.38 | 3.22×10−10 | 5.10× 10−06 | 7.92× 10−11 | 80846547–81597411 | BCKDHB |
rs1421085 | 16 | 53800954 | T/C | − 0.03 | − 0.13 | 6.44× 10−47 | 2.00× 10−05 | 1.97× 10−51 | 53797565–53848561 | FTO |
 rs310011 | 16 | 81471654 | A/G | 0.02 | 0.12 | 1.84×10−11 | 1.90× 10−04 | 2.30× 10−12 | 81449060–81471654 |  |
WHRadjBMI and PCOS | ||||||||||
 rs3767846 | 1 | 214175126 | A/G | 0.02 | 0.13 | 2.12×10−08 | 5.50× 10−04 | 9.99× 10−09 | 214173840–214189783 | PROX1 |
 rs13032835 | 2 | 165748563 | A/T | − 0.03 | − 0.13 | 5.10×10−27 | 5.00× 10−05 | 2.74× 10−30 | 165668018–165828042 | COBLL1, LOC101929633, SLC38A11 |
 rs7774737 | 6 | 81145901 | C/G | − 0.03 | − 0.38 | 4.02×10−08 | 5.10× 10−06 | 8.49× 10−09 | 81145901–81196080 |  |
 rs11057429 | 12 | 124529194 | C/G | − 0.09 | 0.52 | 2.74× 10−09 | 4.20× 10−04 | 4.87× 10−10 | 124529194–124529194 | ZNF664-FAM101A |
 rs310011 | 16 | 81471654 | A/G | 0.02 | 0.12 | 1.20×10−14 | 1.90× 10−04 | 3.06× 10−16 | 81449060–81471654 |  |
CBMI and PCOS | ||||||||||
 rs12641981 | 4 | 45179883 | T/C | 0.04 | 0.10 | 4.19×10−08 | 8.90× 10−04 | 8.24× 10−10 | 45175691–45187622 |  |
 rs10987375 | 9 | 129392365 | T/C | 0.04 | 0.14 | 2.37×10−06 | 3.60× 10−04 | 2.51× 10−08 | 129370576–129397014 | LMX1B |
 rs8050136 | 16 | 53816275 | A/C | 0.07 | 0.15 | 2.24×10−17 | 4.50× 10−06 | 1.56× 10−21 | 53797908–53848561 | FTO |
 rs7228430 | 18 | 57733925 | A/G | 0.05 | 0.12 | 5.02×10−09 | 9.50× 10−04 | 5.50× 10−11 | 57730096–57914679 |  |