Table 3.
Cytoband | SNP | Proxy | Gene | All cancers | ER+ cancers | ER− cancers | ||||
---|---|---|---|---|---|---|---|---|---|---|
Nearest | CHi-C target | P | P adj | P | P adj | P | P adj | |||
2q31.1 | rs1550623 | CDCA7 | CDCA7 | 0.007 | 0.087 | 0.511 | 0.666 | 0.330 | 0.892 | |
11q13.1 | rs3903072 | SNX32 | CTSW | 0.006 | 0.087 | 0.064 | 0.326 | 0.001 | 0.101 | |
11q13.1 | rs3903072 | SNX32 | SNX32 | 0.007 | 0.087 | 0.032 | 0.268 | 0.036 | 0.506 | |
14q13.3 | rs2236007 | rs1018464 | PAX9 | PAX9 | 0.003 | 0.066 | 0.054 | 0.317 | 0.248 | 0.854 |
14q24.1 | rs2588809 | RAD51B | ZFP36L1 | 0.079 | 0.380 | 0.004 | 0.091 | 0.256 | 0.854 | |
17q22 | rs6504950 | rs9902718 | STXBP4 | COX11 | 0.002 | 0.059 | 0.001 | 0.032 | 0.403 | 0.892 |
19p13.11 | rs8170 | rs34084277 | BABAM1, ANKLE1* | MRPL34 | 0.001 | 0.059 | 0.011 | 0.173 | 0.131 | 0.829 |
19p13.11 | rs4808801 | ELL * | LRRC25 | 0.009 | 0.092 | 0.004 | 0.091 | 0.768 | 0.954 | |
19p13.11 | rs4808801 | ELL * | SSBP4 | 0.002 | 0.059 | 0.0002 | 0.016 | 0.475 | 0.892 |
*In an analysis that included all genes that are nearest genes, regardless of whether they were also a CHi-C target gene, rs4808801 was also associated with expression of ELL (FDR adjusted P = 0.05 for all cancers and P = 0.04 for ER+ cancers) and rs8170 was also associated with expression of ANKLE1 (FDR corrected P = 0.05 for all cancers)
PP-value (1df t-test) per allele association with gene expression, adjusted for methylation and copy number, Padj P value further adjusted for multiple testing