Table 2. 5q11.2 SNV association with MAP3K1 and SETD9 gene expression in TCGA-BRCA (ER+) data set.

SNV			MAP3K1 gene expression				SETD9 gene expression
Name/allele	Distance (kbases) from			PIK3CA SM			PIK3CA WT		PIK3CA SM	PIK3CA WT
	MAP3K1	SETD9	Diff. allele +/− (95% CI)	P-value	Diff. allele +/− (95% CI)	P-value	Diff. allele +/− (95% CI)	P-value	Diff. allele +/− (95% CI)	P-value
rs832552 T	<>	−91.2	0.90 (0.46, 1.33)	4.0E−04	0.20 (−0.56, 0.96)	0.57	0.51 (−0.05, 1.08)	0.07	0.06 (−0.91, 0.79)	0.87
rs252913 G	3.9	−9.2	0.77 (0.36, 1.18)	1.0E−03	0.51 (−0.23, 1.25)	0.17	0.64 (0.05, 1.23)	0.04	0.72 (0.19, 1.25)	0.01
rs331499 A	18.9	<>	0.09 (−0.45, 0.61)	0.74	0.30 (−0.06, 0.66)	0.1	0.69 (0.30, 1.08)	0.02	0.81 (0.50, 1.13)	3.0E−06

Abbreviations: <>, inside; Distance, SNV distance from gene start or end (the shortest); PIK3CA SM/WT, in samples with PIK3CA somatic variants/wild type; Diff. allele +/− (95% confidence interval (CI)), difference of the means of gene expression in samples with presence/samples with absence of the allele, with 95% CI; P-value, P-value from Student's t-test.