Table 2.

The most significant association between SNP genotype and UGT2B transcript levels in breast and liver based on two degree of freedom linear models

Tissue and gene	SNP positiona	rs ID	Genotype	No.	Mean log2-transformed transcript levels (s.d.)	P-value	R2
Breast
UGT2B4	69500987	rs2168047	CC	29	−7.2 (1.81)	0.0012	0.160
			CT	33	−10.16 (3.88)
			TT	18	−10.05 (3.81)
UGT2B15	70384595	rs4557343	GG	29	−8.34 (2.16)	0.0018	0.150
			GT	41	−6.82 (2.46)
			TT	11	−5.38 (2.86)
UGT2B17	70038552	rs6822259	CC	2	−13.55 (7.11)	0.0006	0.190b
			TC	14	−12.48 (3.48)
			TT	58	−9.47 (2.41)
	CNV and rs6822259		0 copy	7	−18.44 (0.38)	8.3E-13	0.510
			1/2 copies+CC/TC	16	−12.61 (3.74)
			1/2 copies+TT	58	−9.47 (2.41)
Liver
UGT2B4	70342103	rs12642263	AA	18	−1.85 (1.96)	0.013	0.269
			AG	12	0.23 (1.46)
			GG	1	−2.31
UGT2B7	70482723	rs1835823	GG	21	0.12 (2.01)	0.047	0.196
			GC	9	1.36 (2.11)
			CC	1	4.90
	70320917	rs10007427	CC	14	−0.59 (2.07)	0.019	0.263
			CT	14	1.62 (1.79)
			TT	1	−0.29
UGT2B10	70482723	rs1835823	GG	21	−0.04 (2.37)	0.06	0.182
			GC	9	1.19 (1.95)
			CC	1	5.12
	70320917	rs10007427	CC	14	−0.66 (2.32)	0.056	0.199
			CT	14	1.52 (2.23)
			TT	1	0.36
UGT2B15	69500987	rs2168047	CC	19	−0.49 (1.87)	0.0074	0.296
			CT	10	−2.98 (2.14)
			TT	2	−2.95 (2.00)
	70342103	rs12642263	AA	18	−2.50 (2.18)	0.0027	0.345
			AG	12	0.20 (1.35)
			GG	1	−2.30
UGT2B17	70360475	rs17147338	CC	24	−1.78 (3.20)	0.039	0.214b
			CT	5	−6.01 (3.13)
			TT	1	−3.39
	CNV and rs17147338		0 copy or 1 copy+CT	4	−7.57 (1.35)	2.5E-05	0.530
			2 copies+CT/TT	16	−3.55 (2.46)
			2 copies+CC	11	0.25 (2.88)

Abbreviations: CNV, copy number variation; SNP, single-nucleotide polymorphism.

^aOnly SNPs with call rate >90% were considered.

^bAfter excluding subjects with homozygous deletion of corresponding gene.