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Table 5 Top two-way models identified by ES-MDR in OncoArray-TRICL data

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

Gene(s) 1

SNP 1 (GRCh37/hg19)

Gene Region 1

Alleles (Major/Minor)

MAFa (1000 Genomes)

Gene(s) 2

SNP 2 (GRCh37/hg19)

Gene Region 2

Alleles (Major/Minor)

MAF (1000 Genomes)

ES-MDR Test Score

OncoArray-genotyped (HRa)

Log-rank test statistic

Permutation P value

BRCA1

rs749410065

delTa

–/T

NAa

CBR1, LOC100133286

rs151043730

missense, ncRNAa

G/A

0.001

13.77

1.24

65.74

< 0.0001

BRCA1

rs749410065

delTa

–/T

NAa

NAPG

rs3865365

near 5′ end of genes

G/A

0.06

13.43

1.23

61.74

< 0.0001

C6orf10

rs16870005

Intron

C/T

0.01

BRCA1

rs749410065

delTa

–/T

NAa

13.42

1.25

67.66

< 0.0001

C1orf21, LOC107985236

rs7535067

Intron, 3′ UTRa

C/A,T

0.19

BRCA1

rs749410065

delTa

–/T

NAa

13.39

1.24

61.92

< 0.0001

PSMB9, LOC100294145

rs57092860

Intergenic

T/C,G

0.01

BRCA1

rs749410065

delTa

–/T

NAa

13.37

1.25

67.82

< 0.0001

CTNND2

rs7732411

Intron

T/C

0.08

BRCA1

rs749410065

delTa

–/T

NAa

13.32

1.25

67.53

< 0.0001

TRAM2-AS1, LOC730101

rs182398206

Intergenic

A/G

0.01

BRCA1

rs749410065

delTa

–/T

NAa

13.30

1.25

70.95

< 0.0001

MIR4417, MIR4689

rs6698924

Intergenic

A/C

0.02

BRCA1

rs749410065

delTa

–/T

NAa

13.29

1.25

68.74

< 0.0001

BRCA1

rs749410065

delTa

–/T

NAa

TFAP2C, BMP7

rs186132350

Intergenic

T/A

0.01

13.29

1.25

69.79

< 0.0001

HRAT92, PRKAR1B

rs142263110

Intergenic

G/A

0.002

BRCA1

rs749410065

delTa

–/T

NAa

13.28

1.25

69.36

< 0.0001

  1. aUTR, untranslated region; delTa, NC_000017.10:g.41196821delT; ncRNA, noncoding transcript variant; HR, hazard ratio; NA, not available