Table 2.
Results of posterior probability analysis
| Region | Index SNP (locus) | Chromosome | SNPs in PPS (proportion) | Proportion of SNPs in PPS (all SNPs) according to functional annotationa | |||
|---|---|---|---|---|---|---|---|
| High impact | Moderate impact | Low impact | Modifier impact | ||||
| 1 | rs13387042 (2q35) | 2 | 42 (0.04) | 0 (0) | 0 (0) | 0 (0) | 1 (1.00) |
| 2 | rs10069690 (TERT) | 5 | 224 (0.74) | 0 (0) | 0.009 (0.01) | 0.027 (0.023) | 0.964 (0.967) |
| 3 | rs889312 (MAP3K1) | 5 | 802 (0.58) | 0 (0) | 0.005 (0.005) | 0.012 (0.012) | 0.983 (0.983) |
| 4 | rs2046210 (ESR1) | 6 | 455 (0.44) | 0 (0) | 0.026 (0.019) | 0.009 (0.01) | 0.965 (0.971) |
| 5 | rs1562430 (8q24) | 8 | 2954 (0.59) | 0 (0) | 0.001 (0.003) | 0.001 (0.001) | 0.997 (0.996) |
| 6 | rs10995190 (ZNF365) | 10 | 716 (0.41) | 0 (0) | 0.007 (0.006) | 0 (0.003) | 0.993 (0.992) |
| 7 | rs704010 (ZMIZ1) | 10 | 2108 (0.72) | 0 (0) | 0.001 (0.001) | 0.007 (0.005) | 0.992 (0.994) |
| 8 | rs2981579 (FGFR2) | 10 | 2827 (0.59) | 0.0004 (0.0002) | 0.01 (0.011) | 0.007 (0.008) | 0.982 (0.981) |
| 9 | rs614367 (11q13) | 11 | 11 (0.007) | 0 (0) | 0 (0.007) | 0 (0.002) | 1 (0.990) |
| 10 | rs999737 (RAD51B) | 14 | 2451 (0.77) | 0 (0.0003) | 0.004 (0.005) | 0.003 (0.003) | 0.993 (0.991) |
| 11 | rs3803662 (TOX3) | 16 | 850 (0.55) | 0 (0) | 0.001 (0.003) | 0.007 (0.006) | 0.992 (0.991) |
| 12 | rs8170 (MERIT40) | 19 | 2274 (0.79) | 0 (0) | 0.035 (0.035) | 0.049 (0.047) | 0.916 (0.917) |
PPS Posterior probability set, SNP Single-nucleotide polymorphism
Results are shown for PPSs and proportions of PPS SNPs by functional annotations compared with the overall distribution of annotations by region
aAs defined by SnpEff [43]