Table 3.
Annotation of possible ‘functional’ SNPs using lead SNP approach in (A) RegulomeDB (61) and (B) HaploReg (60)
| Lead SNP | chr | Position (hg19) | Associated gene | Highest SNP in LD | RegulomeDB score | Position (hg19) | Distance to lead SNP (bp) |
|---|---|---|---|---|---|---|---|
| (A) | |||||||
| rs6448050 (discovery) | 4 | 21407759 | KCNIP4 | rs59708864 | 3a | 21368138 | 39621 |
| rs9799795 (fine mapping) | 4 | 20831806 | KCNIP4 | rs923673 | 1f | 20791197 | 40609 |
| rs11662168 (discovery) | 18 | 30026392 | GAREM | rs7237059 | 2b | 29958797 | 67595 |
| rs3786309 (fine mapping) | 18 | 29972774 | GAREM | rs73956883 | 2b | 29913973 | 58801 |
| Lead SNP | chr | Position (hg19) | Associated gene | Highest SNP in LD | HaploReg results | Position (hg19) | Distance to lead SNP (bp) |
|---|---|---|---|---|---|---|---|
| (B) | |||||||
| rs6448050 (discovery) | 4 | 21407759 | KCNIP4 | rs17462464 | 16 regulatory motifs altered | 21383391 | 24368 |
| rs9799795 (fine mapping) | 4 | 20831806 | KCNIP4 | rs11727733 | Foxp3 regulatory motif altered | 20837717 | 5911 |
| rs11662168 (discovery) | 18 | 30026392 | GAREM | rs10468834 | p53 regulatory motif altered | 30029959 | 3567 |
| rs3786309 (fine mapping) | 18 | 29972774 | GAREM | rs3786309 | RXRA motif altered | — | — |
Regulome scores correspond to 1f, eQTL + TF binding/DNase peak; 2a, TF binding + matched TF motif + matched DNase Footprint + DNase peak; 2b, TF binding + any motif + DNase Footprint + DNase peak; 3a, TF binding + any motif + DNase peak. Table 3B highlights the variants that may impact the function of genes known to be relevant in lung cancer development and/or progression. For rs3786309, HaploReg did not yield any functional SNPs in their LD algorithm.