Table 2 Eleven novel loci associated with abundance from Discovery GWAS and Meta-analyses with p < 5 × 10− 6â€
From: Germline genetic regulation of the colorectal tumor immune microenvironment
RSID: CHR: BP | Nearest Gene | Loci | EFF/REF Alleles* | Discovery (MECC) | Replication (CLX) | Replication (CRCGEN) | Meta Analysis | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EAF** | OR (95% CI)*** | p | EAF | OR (95% CI)*** | p | EAF | OR (95% CI)*** | p | EAF | OR (95% CI)*** | p | PHeterogeneity | ||||
rs1518405:2:181016277 | CWC22 | 2q31.3 | A/T | 0.97 | 1.59 (1.32–1.91) | 8.67E-07 | 0.97 | 1.74 (0.74–4.07) | 0.2054 | 0.99 | 0.97 (0.14–6.56) | 0.9737 | 0.97 | 1.59 (1.33–1.90) | 4.08E-07 | 0.8602 |
rs144595725:14:31526087 | AP4S1 | 14q12 | A/G | 0.99 | 2.71 (1.82–4.03) | 9.37E-07 | NA | NA | NA | 0.99 | 3.96 (0.18–88.64) | 0.3871 | 0.99 | 2.73 (1.84–4.05) | 6.11E-07 | 0.8129 |
rs56148061:11:61014040 | PGA4:PGA5 | 11q12 | A/C | 0.04 | 0.60 (0.49–0.74) | 1.30E-06 | 0.95 | 0.45 (0.18–1.08) | 0.0766 | 0.95 | 2.45 (0.42–14.31) | 0.3218 | 0.04 | 0.60 (0.50–0.74) | 6.12E-07 | 0.2381 |
rs147844733:17:36994755 | C17orf98 | 17q12 | A/T | 0.99 | 2.35 (1.68–3.28) | 5.54E-07 | NA | NA | NA | 1.00 | 0.36 (0.01–19.56) | 0.6191 | 0.99 | 2.32 (1.66–3.23) | 6.99E-07 | 0.3604 |
rs142105062:11:122506047 | RP11-266E8.2 | 11q13.1 | T/C | 0.01 | 0.17 (0.09–0.34) | 4.29E-07 | NA | NA | NA | 0.01 | 1.04 (0.09–12.46) | 0.9727 | 0.01 | 0.20 (0.10–0.38) | 1.04E-06 | 0.1728 |
rs577783:6:137918440 | BTF3L4P3 | 6q23.3 | A/G | 0.37 | 0.85 (0.80–0.91) | 1.36E-06 | 0.45 | 1.08 (0.80–1.46) | 0.6240 | 0.41 | 0.68 (0.45–1.03) | 0.0722 | 0.63 | 0.86 (0.80–0.91) | 1.23E-06 | 0.1791 |
rs9770081:7:622706 | PRKAR1B | 7p22.3 | T/G | 0.25 | 0.80 (0.74–0.88) | 6.11E-07 | NA | NA | NA | 0.35 | 1.82 (0.92–3.62) | 0.0887 | 0.25 | 0.81 (0.75–0.89) | 2.01E-06 | 0.0206 |
rs12313375:12:94976499 | TMCC3 | 12q22 | A/C | 0.98 | 0.58 (0.46–0.73) | 4.56E-06 | 0.98 | 0.70 (0.23–2.10) | 0.5270 | 0.99 | 0.29 (0.04–1.97) | 0.2053 | 0.98 | 0.58 (0.46–0.73) | 2.10E-06 | 0.7284 |
rs135429:22:44657217 | KIAA1644 | 22q13.31 | T/C | 0.31 | 0.85 (0.79–0.91) | 2.49E-06 | 0.36 | 0.86 (0.58–1.26) | 0.4301 | 0.36 | 1.02 (0.66–1.58) | 0.9114 | 0.31 | 0.85 (0.80–0.91) | 2.43E-06 | 0.7032 |
rs4495475:8:66165989 | RPL31P41 | 8q13.1 | A/C | 0.80 | 1.21 (1.12–1.30) | 1.25E-06 | 0.82 | 1.03 (0.69–1.53) | 0.8851 | 0.81 | 0.86 (0.49–1.51) | 0.6014 | 0.80 | 1.19 (1.11–1.29) | 2.73E-06 | 0.3817 |
rs190417185:2:74892755 | SEMA4F | 2p13.1 | T/C | 0.02 | 2.08 (1.53–2.82) | 2.48E-06 | NA | NA | NA | 0.01 | 0 (0.00-3.94) | 0.1030 | 0.02 | 2.06 (1.52–2.79) | 3.18E-06 | 0.0703 |