Table 4 Putative Role of the associated variants with NSCLC in JandK Population—North India using the information from the different online 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
rs12190287	C/G	TCF21	Lung	515	0.29	1.9E − 17	1	Significant and Up regulation	3_TxFlnk/3_PromD1/H3K4me1_Enh/H3K4me3_Pro/H3K27ac_Enh/H3K9ac_Pro/23_PromBiv	Creation of new site/ broken site for 9G8
rs751402	A/G	ERCC5	Lung	515	0.14	6.2E − 4	1	Significant and Up regulation	1_TssA/H3K4me3_Pro/H3K27ac_Enh/H3K9ac_Pro/H3K4me1_Enh/DNase	Creation of new site for Tra2-β/ broken site for SRp40
rs4986764	A/G	BRIP1	Lung	515	− 0.09	3.8E − 3	0.985	Significant and Down regulation	NA	Site broken for SRp40
rs2298881	A/C	ERCC1	Lung	515	− 0.36	2.4E − 15	1	Significant and Down regulation	1_TssA/3_PromD1/H3K4me1_Enh/H3K4me3_Pro/H3K27ac_Enh/H3K9ac_Pro DNase hypersensitive	Site broken for SRp40
rs4757151	A/G	ARNTL/BTBD10	Lung	515	0.002	0.9	0.04	Not Significant	H3K4me1_Enh	Creation of new site/broken site for SC35
rs11615	G/A	ERCC1	Lung	515	− 0.05	0.1	0.6	Not Significant	11_TxEnh3/H3K4me1_Enh/H3K27ac_Enh/6_EnhG	Creation of new site/ broken site for SF2/ASF (IgM/BRCA1), SF2/ASF and G98
rs11615	G/A	CD3EAP	Lung	515	− 0.14	4.8E − 7	1	Significant and down regulation	11_TxEnh3/H3K4me1_Enh/H3K27ac_Enh/6_EnhG

*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; H3K27Ac_Enh—chemical modification (acetylation) of the histone proteins (H3) at lysine 27 and associated with transcriptional initiation and open chromatin structure (active enhancer); H3K4me3–chemical modification (methylation) of the histone proteins (H3) at lysine 4, marks promoters that are active or poised to be activated; H3K4me1—chemical modification (methylation) of the histone proteins (H3) at lysine 4 and is associated with enhancers, and downstream of transcription starts.; H3K9ac—chemical modification (acetylation) of the histone proteins (H3) at lysine 9 and is associated with transcriptional initiation and open chromatin structure; Enh—Enhancers; Pro—Promoters; TSSA—active transcription start site; TxReg—transcription regulatory; PromD1—promoter downstream TSS; TSSAFlk—Flanking TSS; 22PromP—poised promoter; EnhW1—weak enhancer; EnhA2—active enhancer 2; the H3K4me1/2/3 and H3K36me2/3 are linked with genomic region which actively transcribing and H3K9me3, H3K27me3 and H4K20me3 with non-transcribing region; ESE—Exonic Splicing Enhancers; SR—Serine-Arginine rich proteins; 9G8, SC35—SR splicing factor; SF2/ASF (IgM-BRCA1)—Serine-Arginine rich proteins.

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