Table 4.
Statistical fine-mapping prioritized the potential causal SNP within 10 independent cross-cancer signals in 5p15.33 region, using PAINTOR v.3.0
| Index SNP | Fine-mapped cancer types | Fine-mapping without functional prior |
Fine-mapping with functional priora |
||||||
|---|---|---|---|---|---|---|---|---|---|
| 95% PP credible setb | PP, index SNP | SNP with highest PP | Highest PP | 95% PP credible set | PP, index SNP | SNP with highest PP | Highest PP | ||
| rs35033501 (5:1253918:C:T) | ER-neg BrCa, lung, melanoma, pancreatic, prostate | rs35033501, rs71595003 | 0.875 | rs35033501 (5:1253918:C:T) | 0.875 | rs71595003 | <0.001 | rs71595003 (5:1292118:G:A) | 0.999 |
| rs192723047 (5:1273183:A:G) | ER-neg BrCa, prostate | rs192723047 | 1.000 | rs192723047 (5:1273183:A:G) | 1.000 | rs192723047 | 1.000 | rs192723047 (5:1273183:A:G) | 1.000 |
| rs10069690 (5:1279790:C:T) | ER-neg BrCa, glioma, ovarian, pancreatic, prostate | rs10069690 | 1.000 | rs10069690 (5:1279790:C:T) | 1.000 | rs10069690 | 1.000 | rs10069690 (5:1279790:C:T) | 1.000 |
| rs7705526 (5:1285974:C:A) | ER-neg BrCa, colorectal, glioma, lung, melanoma, ovarian, pancreatic, prostate | rs7705526 | 1.000 | rs7705526 (5:1285974:C:A) | 1.000 | rs7705526 | 1.000 | rs7705526 (5:1285974:C:A) | 1.000 |
| rs2853677 (5:1287194:G:A) | ER-neg BrCa, colorectal, glioma, lung, melanoma, ovarian, pancreatic, prostate | rs2853677 | 1.000 | rs2853677 (5:1287194:G:A) | 1.000 | rs2853677 | 1.000 | rs2853677 (5:1287194:G:A) | 1.000 |
| rs11414507 (5:1291331:A:AC) | ER-neg BrCa, prostate | rs7712562, rs74682426, rs11414507, rs7449190 | 0.265 | rs7712562 (5:1296072:A:G) | 0.367 | rs7712562, rs11414507 | 0.419 | rs7712562 (5:1296072:A:G) | 0.581 |
| rs35334674 (5:1292299:G:A) | ER-neg BrCa, colorectal, glioma, lung, pancreatic, prostate | rs35334674 | 0.987 | rs35334674 (5:1292299:G:A) | 0.987 | rs35334674 | 0.988 | rs35334674 (5:1292299:G:A) | 0.988 |
| rs35226131 (5:1295373:C:T) | colorectal, glioma, pancreatic, prostate | rs35226131, rs35161420, rs61748181, rs33958877, rs114616103 | 0.273 | rs35226131 (5:1295373:C:T) | 0.273 | rs35226131, rs35161420, rs61748181, rs33958877, rs114616103 | 0.273 | rs35226131 (5:1295373:C:T) | 0.273 |
| rs3888705 (5:1298645:G:A) | ER-neg BrCa, colorectal, ovarian, pancreatic, prostate | rs34156553, rs4075202, rs3888705, rs77776598, rs4975539, rs6875445, rs4583925, rs78844046, rs79323805, rs4507531, rs78368589, rs4487533, rs6554678, rs4498293, rs4532396 | 0.092 | rs34156553 (5:1243245:C:T) | 0.103 | rs34156553, rs4075202, rs3888705, rs77776598, rs4975539, rs6875445, rs4583925, rs78844046, rs79323805, rs4507531, rs78368589, rs4487533, rs6554678, rs4498293, rs4532396 | 0.092 | rs34156553 (5:1243245:C:T) | 0.103 |
| rs465498 (5:1325803:A:G) | lung, melanoma, pancreatic | rs380286, rs421629, rs465498, rs452932, rs459961, rs455433, rs13178866, rs460073 | 0.146 | rs380286 (5:1320247:G:A) | 0.462 | rs421629, rs465498 | 0.437 | rs421629 (5:1320136:G:A) | 0.563 |
a
Used open chromatin narrow peaks identified from the normal tissue or primary cells of the disease-related organs as the functional prior. Open chromatin narrow peaks were obtained from the ENCODE project.
b
SNPs within the credible set were ranked by the posterior probability (PP).