Table 3

List of top 20 SNP differences in clearance and non-clearance patients

	Gene name	SNP ID	SNP in chromosome	Minor allele	Major allele	Frequency in clearance	Frequency in controls	p Value	OR	Function
1	TNR	rs2239818	chr1_173642258	A	G	0.01	0.22	1.28E−05	0.04	Receptor binding; negative regulation of cell adhesion
2	SPINT2	rs3745948	chr19_43471696	T	C	0.05	0.33	1.46E−05	0.12	Serine-type endopeptidase inhibitor activity
3	TNR	rs34842046	chr1_173559295	T	A	0.02	0.22	6.67E−05	0.08	Receptor binding; negative regulation of cell adhesion
4	HTR3E	rs7627615	chr3_185301110	G	A	0.35	0.04	8.81E−05	11.69	Receptor activity; extracellular ligand-gated ion channel activity
5	TMPRSS11A	rs1370840	chr4_68492841	A	G	0.31	0.02	0.000157	18.97	TMPRSS11A expression in normal oesophagus, liver, colon and lung, with downregulated expression in tumours
6	TMPRSS11A	rs11930532	chr4_68494878	C	T	0.29	0.02	0.000159	18.91	TMPRSS11A expression in normal oesophagus, liver, colon and lung, with downregulated expression in tumours
7	TMPRSS11A	rs28437478	chr4_68493016	A	T	0.29	0.02	0.000189	18.53	TMPRSS11A expression in normal oesophagus, liver, colon and lung, with downregulated expression in tumours
8	SALL2	rs1263810	chr14_21061466	G	C	0.16	0.45	0.000206	0.23	DNA binding; sequence-specific DNA binding transcription factor activity
9	SPATA 22	rs9901726	chr17_3290284	T	C	0.02	0.19	0.000223	0.09	SPATA22
10	SPATA 22	rs2291604	chr17_3299188	G	C	0.02	0.19	0.000223	0.09	SPATA 22
11	NMNAT2	rs607332	chr1_181519836	A	G	0.18	0.48	0.000227	0.24	Nucleotide binding; nicotinamide-nucleotide adenylyltransferase activity
12	NCKAP1	Novel	chr2_183540400	T	C	0.03	0.22	0.000266	0.11	Protein binding; plasma membrane; apoptosis
13	SPATA 22	rs9900543	chr17_3296435	C	T	0.02	0.19	0.000316	0.09	SPATA 22
14	NCKAP1	Novel	chr2_183501325	T	C	0.03	0.22	0.000319	0.12	Protein binding; plasma membrane; apoptosis
15	MARVELD3	rs2303225	chr16_70232383	C	G	0.42	0.11	0.000333	5.61	Membrane; integral to membrane;
16	TMPRSS11A	rs6552134	chr4_68511802	G	A	0.27	0.02	0.00048	16.25	TMPRSS11Aexpression in normal oesophagus, liver, colon and lung, with downregulated expression in tumours
17	ZNF491	Novel	chr19_11778746	A	C	0.01	0.15	0.000525	0.06	DNA binding; zinc ion binding
18	ZNF440	Novel	chr19_11804552	A	G	0.01	0.15	0.000525	0.06	DNA binding; zinc ion binding
19	ZNF439	Novel	chr19_11840305	G	C	0.01	0.15	0.000525	0.06	DNA binding; zinc ion binding
20	CA2	rs2307075	chr8_86575480	C	A	0.34	0.66	0.000528	0.27	Kidney development; morphogenesis of an epithelium; carbonate dehydratase activity; protein binding

CA2, carbonate dehydratase II; HTR3E, 5-hydroxytryptamine receptor 3 family member E; MARVELD3, MARVEL domain containing 3; NCKAP1, NCK-associated protein 1; NMNAT2, nicotinamide mononucleotide adenylyltransferase 2; SALL2, sal-like protein 2; SNP, single nucleotide polymorphism; SPATA 22, spermatogenesis associated 22; SPINT2, serine peptidase inhibitor, kunitz type 2; TMPRSS11A, transmembrane protease, serine 11A; TNR, tenascin receptor; ZNF, zinc finger protein;