Table 3.
Results for forward selection and elastic-net analyses for SNPs selected by both methods
| Cytogenetic band |
Nearest genomic featureA |
Accession number (bp position, hgl9) |
Accession number for equivalent previously published SNP (bp position, hgl9) |
Forward selection co-efficient (standard error) |
Elastic-net co-efficient |
|---|---|---|---|---|---|
| 6q25.3 | SLC22A3 | *rs3123636 (160.84 Mb) | ars9364554 (160.83 Mb) | 0.28 (0.05) | 0.005 |
| 8q24.21 | Intergenic (10 kb upstream of PCAT2) | *rs77541621 (128.08 Mb) | brs6983561 (128.10 Mb) | 0.68 (0.15) | 0.103 |
| PRNCR1 | *rs56005245 (128.11 Mb) | crsl6901979 (128.12 Mb) | 0.39 (0.07) | 0.036 | |
| Intergenic, 50Kb downstream of PRNCR1, 50-kb upstream of CASC19 |
rs2392725 (128.16 Mb) | Unreported | −0.29 (0.05) | −0.018 | |
| CASC19 | *rsl38042437 (128.208 Mb) | drsl88140481 (128.19 Mb) | 2.21 (0.46) | 0.143 | |
| 400 bases downstream of CASC19 | rs79797202 (128.210 Mb) | Unreported | −0.47 (0.14) | −0.016 | |
| Intergenic, 10-kb downstream of CASC19 | rsl44940621 (128.215 Mb) | Unreported | 0.88 (0.27) | 0.096 | |
| CASC8/CASC21 | *rs4506170 (128.32 Mb) | ers620861 (128.34 Mb) | 0.31 (0.07) | 0.027 | |
| CASC8 | rsl2682374 (128.41 Mb) | frs6983267 (128.41 Mb) | −0.19 (0.05) | −0.004 | |
| Intergenic, 20-kb downstream of CASC8 | rs7841251 (128.52 Mb) | grs1447295 (128.48 Mb) | −0.26 (0.07) | −0.012 | |
| 10q11.23 | TIMM23 | *rsl0763567 (51.54 Mb) | grsl0993994 (51.49 Mb) | −0.27 (0.05) | – |
| rs72795883 (51.57 Mb) | – | 0.26 | |||
| 11ql3.3 | Intergenic (75-kb upstream of MYEOV) | *rsl2270641 (69.01 Mb) | ars7931342 (68.99 Mb) | 0.33 (0.05) | 0.024 |
| 17q12 | HNF1B | *rs11651052 (36.10Mb) | hrs4430796 (36.10 Mb) | 0.31 (0.05) | 0.044 |
*
SNP was significant in the genome-wide association of all prostate cancer cases versus controls
References:
A
Refseq annotation names