Table 4.
Putative Role of the associated variants with non-small cell lung cancer in J&K, North- India utilizing the information from the various databases, including GTEX, UCSC genome browser and HSF
| Variant | Allele Ref/Alt |
eQTL gene | eQTL Tissue | eQTL sample size | eQTL NES | eQTL p-value |
eQTL m-value |
Putative role (cis- eQTL) of variant | Regulatory role of variant (ENCODE and Haploreg data) | Splicing effect |
|---|---|---|---|---|---|---|---|---|---|---|
| rs10228682 | C/T* | POT1-AS1 | Lung | 515 | 0.45 | 2.2E-18 | 1 | Significant and Up regulation | NA | Broken site for 9G8 |
| rs10069690 | *T/C | TERT | Lung | NA | NA | NA | NA | NA | NA |
Creation of new site/ broken site for SF2/ASF (IgM/BRCA1), SF2/ASF and SRp40 |
| rs251796 | *A/G | TERF2 | Lung | 515 | -0.470 | 1.3E-19 | 1 | Significant and down regulation | NA | NA |
| rs2975843 | *A/G | TERF2 | Lung | 515 | -0.067 | 0.07 | 0.988 | Down regulated and non-significant | H3K4me3_Pro, H3K4me1_Enh | NA |
*represents risk allele in this study, NES Normalized Effect Size in Eqtl, m-value Posterior probability that effect exists in each tissue, ranges between 0 and 1, ESE Exonic Splicing Enhancers, SR Serine-Arginine rich proteins, 9G8, SC35 SR splicing factor, SF2/ASF (IgM-BRCA1) Serine-Arginine rich proteins. H3K4me3 Chemical modification (methylation) of the histone proteins (H3) at lysine 4, marks promoters that are active or poised to be activated, Enh Enhancers, Pro Promoters