Table 1 Chromatin States and risk allele prediction of DHS-SNVs as cis-eQTLs of the target genes belonging to Xenobiotic metabolism and DNA repair pathway.
Gene symbol | SNP | p-value | Effect size | Tissue | Predicted risk allele | cancer type | Beta (β) | t-stat | p-value | Risk alleles in lung cancer | The Chromm States in the lung (25-core model) |
|---|---|---|---|---|---|---|---|---|---|---|---|
[I] Xenobiotic metabolism genes | |||||||||||
SULT1A1 | rs743590 | 2.00E−11 | − 0.37 | Lung | G | LUAD | − 0.2 | − 4.02 | 6.68E−05 | G | Active Enhancer 1 |
SULT1A1 | rs3760091 | 1.40E−12 | 0.36 | Lung | G | No data | No data | No data | No data | No data | Promoter Upstream of TSS |
SULT1A1 | rs112411210 | 0.012 | 0.38 | Lung | A | No data | No data | No data | No data | No data | Active Enhancer 2 |
GSTA1 | rs10948723 | 4.00E−07 | − 0.15 | Lung | C | LUAD | 0.35 | 8.04 | 6.92E−15 | C | Quiescent |
SULT1A2 | rs743590 | 5.50E−06 | 0.21 | Lung | A | No data | No data | No data | No data | No data | Active Enhancer 1 |
GSTA1 | rs2207950 | 6.80E−05 | 0.12 | Lung | A | LUAD | 0.27 | 5.94 | 5.39E−09 | A | Quiescent |
GSTA4 | rs1802061 | 0.0015 | − 0.15 | Lung | T | No data | No data | No data | No data | No data | Quiescent |
ALDH3B1 | rs3764821 | 0.0023 | − 0.08 | Lung | G | No data | No data | No data | No data | No data | Promoter Downstream of TSS 1 |
SULT1A2 | rs3760091 | 0.023 | − 0.097 | Lung | C | No data | No data | No data | No data | No data | Promoter Upstream of TSS |
GSTO1 | rs12250592 | 0.027 | 0.13 | Lung | C | No data | No data | No data | No data | No data | Promoter Downstream of TSS 1 |
GSTO1 | rs17883150 | 0.00085 | 0.078 | Lung | G | No data | No data | No data | No data | No data | Primary DNase site |
GSTA4 | rs4986947 | 0.0015 | − 0.15 | Lung | A | No data | No data | No data | No data | No data | Quiescent |
SULT1A2 | rs13331376 | 0.0058 | − 0.39 | Lung | T | No data | No data | No data | No data | No data | Promoter Upstream of TSS |
GSTO1 | rs7083465 | 0.027 | 0.13 | Lung | G | No data | No data | No data | No data | No data | Primary H3K27ac possible Enhancer |
MAFG | rs35568625 | 0.042 | − 0.043 | Lung | C | No data | No data | No data | No data | No data | Quiescent |
[II] DNA Repair genes | |||||||||||
RAD52 | rs3748523 | 2.50E−28 | − 0.39 | Lung | G | No data | No data | No data | No data | No data | Active TSS |
EME2 | rs238679 | 0.00017 | − 0.11 | Lung | G | No data | No data | No data | No data | No data | Quiescent |
EME2 | rs1625393 | 0.0012 | − 0.13 | Lung | G | No data | No data | No data | No data | No data | Quiescent |
ERCC5 | rs4150276 | 0.0009 | 0.094 | Lung | T | No data | No data | No data | No data | No data | Quiescent |
MUTYH | rs2153608 | 0.012 | − 0.091 | Lung | G | No data | No data | No data | No data | No data | Weak Enhancer 2 |
MUTYH | rs3219472 | 0.026 | − 0.082 | Lung | T | No data | No data | No data | No data | No data | Quiescent |
POLM | rs11764344 | 1.40E−11 | − 0.38 | Lung | C | No data | No data | No data | No data | No data | Quiescent |
PMS1 | rs5742926 | 0.00013 | 0.15 | Lung | G | LUSC | 0.29 | 4.11 | 4.72E−05 | G | Promoter Downstream of TSS 1 |
MLH1 | rs145070498 | 0.01 | − 0.12 | Lung | T | No data | No data | No data | No data | No data | Promoter Upstream of TSS |
