Table 2.
Enrichment of prostate cancer (PrCa) GWAS signals with p value < 10−8 for non-prostate-related annotations before and after removing SNPs overlapping with corresponding annotation in LNCaP
| Non-prostate DHS with top enrichment of PrCa GWAS signals | % of SNPs overlap with LNCaP DHS | Enrichment (95% CI) before removal | p value before removal | Enrichment (95% CI) after removal | p value after removal |
|---|---|---|---|---|---|
| Fetal large intestine tissue | 41.02 | 3.02 (2.21–4.12) | 3.51E−12 | 3.00 (1.63–5.54) | 4.3E−04 |
| CACO-2 cell line, colorectal cancer | 23.10 | 2.89 (2.20–3.78) | 1.33E−14 | 1.94 (1.15–3.25) | 0.01 |
| Fetal small intestine tissue | 35.19 | 2.85 (2.17–3.75) | 7.21E−14 | 2.72 (1.63–4.54) | 1.4E−04 |
| Hep-G2 cell line, liver cancer | 41.38 | 2.78 (2.05–3.77) | 5.57E−11 | 1.51 (0.74–3.07) | 0.26 |
| MCF-7 cell line, breast cancer | 44.57 | 2.70 (1.95–3.74) | 2.19E−09 | 2.26 (1.07–4.78) | 0.03 |
| Fetal stomach tissue | 31.26 | 2.61 (2.01–3.39) | 7.58E−13 | 2.14 (1.31–3.50) | 0.002 |
| GM12878 cell line, lymphocyte | 29.79 | 2.58 (1.93–3.45) | 1.80E−10 | 1.22 (0.64–2.33) | 0.55 |
| CD3 cell, blood | 37.41 | 2.54 (1.86–3.47) | 5.07E−09 | 0.77 (0.31–1.93) | 0.58 |
| hTH2 cell, blood | 32.14 | 2.52 (1.87–3.40) | 1.69E−09 | 1.10 (0.52–2.31) | 0.80 |
| GM06990 cell line, lymphocyte | 29.89 | 2.52 (1.87–3.39) | 1.19E−09 | 1.13 (0.56–2.28) | 0.74 |
| Non-prostate super enhancer with top enrichment of PrCa GWAS signals | % of SNPs overlap with LNCaP super enhancer | Enrichment (95% CI) before removal | p value before removal | Enrichment (95% CI) after removal | p value after removal |
| VACO 9M cell line, colorectal cancer | 8.30 | 7.67 (5.13–11.46) | 3.48E−23 | 8.06 (5.27–12.34) | 7.63E−22 |
| VACO 400 cell line, colorectal cancer | 9.95 | 5.59 (3.46–9.03) | 1.87E−12 | 6.01 (3.62–9.98) | 3.77E−12 |
| Colorectal cancer crypt tissue | 13.07 | 5.43 (3.44–8.56) | 3.52E−13 | 4.03 (2.78–5.84) | 1.71E−13 |
| Thymus tissue | 5.64 | 5.05 (2.95–8.66) | 3.76E−09 | 5.57 (3.25–9.55) | 4.10E−10 |
| Pancreas tissue | 17.76 | 4.66 (2.81–7.72) | 2.47E−09 | 5.77 (3.37–9.89) | 1.86E−10 |
| CD19 cell, blood | 3.08 | 4.53 (2.78–7.40) | 1.52E−09 | 4.76 (2.92–7.78) | 4.44E−10 |
| GM12878 cell line, leukemia | 2.07 | 4.37 (2.25–8.50) | 1.37E−05 | 4.55 (2.34–8.86) | 7.90E−06 |
| HCT-116 cell line, colorectal cancer | 7.19 | 3.68 (1.96–6.93) | 5.20E−05 | 3.47 (1.72–7.02) | 5.25E−04 |
| Gastric tissue | 16.15 | 3.66 (2.57–5.22) | 8.61E−13 | 4.03 (2.78–5.84) | 1.71E−13 |
| CD20 cell, blood | 3.21 | 3.35 (2.26–4.96) | 1.92E−09 | 3.49 (2.36–5.18) | 5.01E−10 |
| Sigmoid colon tissue | 12.78 | 3.30 (2.21–4.93) | 5.97E−09 | 3.58 (2.36–5.43) | 2.04E−09 |
| HCC-1954 cell line, breast cancer | 4.27 | 3.30 (1.85–5.89) | 5.07E−05 | 2.99 (1.59–5.62) | 6.59E−04 |
| Duodenum smooth muscle tissue | 6.75 | 3.23 (2.03–5.15) | 7.31E−07 | 3.35 (2.08–5.40) | 6.54E−07 |
| CD56 cell, blood | 4.42 | 2.93 (1.71–5.01) | 8.89E−05 | 3.10 (1.81–5.30) | 3.65E−05 |
| Fetal large intestine tissue | 8.16 | 2.83 (1.82–4.40) | 4.28E−06 | 2.87 (1.81–4.57) | 8.51E−06 |
Only annotations with statistical significance and 2.5+ fold of enrichment before removal are listed