A new efficient method to detect genetic interactions for lung cancer GWAS

BMC Medical Genomics

Table 6 Top SNPs selected by cox lasso regression in OncoArray-TRICL data

Nearest Gene(s)	Chr^a	SNP (GRCh37/hg19)	Position (bp^a) (GRCh37/hg19)	Gene region	Alleles (Major/Minor)	MAF^a (1000 Genomes)	Test score	OncoArray-genotyped (HR^a)	Permutation P value
BRCA1	17	rs749410065	41196821	delT^a	–/T	NA^a	62.20	1.24	< 0.0001
GTF2IP1, PMS2P5	7	rs149743903	35528378	Intergenic	C/G	NA^a	295.80	6.39	< 0.0001
LOC102467079, TOX3	16	rs117142114	52328666	Intergenic	T/C	0.02	31.00	1.29	< 0.0001
HYKK	15	rs9788721	78802869	Intron	C/T	0.31	86.30	1.41	< 0.0001
MIR3925, PANDAR	6	rs7753169	36614326	Intergenic	A/C	0.36	27.90	1.15	< 0.0001
CHRNA5	15	rs16969968	78882925	missense	G/A	0.15	86.80	1.41	< 0.0001
KLF5, LINC00392	13	rs138428539	73736950	Intergenic	T/C,G	0.01	145.10	6.46	< 0.0001
TULP1, FKBP5	6	rs6906359	35528378	Intron	C/T	0.10	135.90	5.76	< 0.0001
CHRNA5	15	rs951266	78878541	Intron	G/A	0.16	88.50	1.41	< 0.0001
FAM114A1	4	rs1873195	38891173	Intron	C/T	0.20	8.90	0.87	0.0119

^aChr, chromosome; NA, not available; bp, base pair; delT^a = NC_000017.10:g.41196821delT; MAF, minor allele frequency; HR, hazard ratio

ISSN: 1755-8794