Table 5.

Putative transcription factor binding sites altered by 5′-UTR and regulatory region SNPs

Affymetrix probe-set ID	c3-eQTL	SNPa	Distance from TSSb	Predicted Transcription Factor Site	P BNc	P SHRd	Ratio (BN/SHR)e	Log Ratiof
1393902_at	Akr1c1	T>A	−1716	Hmgiγ	7.90E-04	3.10E-02	0.026	−1.59
1387819_at	Cela1	T>C	−1747	Xpf1	2.80E-03	4.90E-02	0.056	−1.25
1387819_at	Cela1	A>T	−2463	Pax	8.70E-03	1.80E-01	0.049	−1.31
1370269_at	Cyp1a1	A>G	−563	Ahr	2.50E-04	8.80E-06	28.4	1.45
1370269_at	Cyp1a1	C>T	−1735	Spz1	1.30E-03	8.50E-02	0.015	−1.83
1370148_at	Hp	G>T	−1735	Gata1	2.90E-01	2.10E-03	137.9	2.14
1370148_at	Hp	G>T	−2882	Gata1	2.40E-01	1.80E-03	135	2.13
1370148_at	Hp	A>T	−3293	Gata1	2.10E-01	2.40E-03	88.5	1.95
1370148_at	Hp	A>T	−3293	Lmo2com	2.40E-01	3.60E-03	68.1	1.83
1370148_at	Hp	A>T	−3293	Gata2	3.30E-01	4.90E-03	67.2	1.83
1370148_at	Hp	G>A	−79	Cebp	8.70E-02	2.00E-03	43.1	1.63
1370148_at	Hp	G>T	−3789	Pax	3.30E-04	5.40E-03	0.061	−1.21
1370148_at	Hp	C>T	−2290	Taxcreb	2.00E-03	5.10E-02	0.038	−1.41
1370148_at	Hp	A>T	−3293	Cdpcr3 hd	5.00E-03	2.70E-01	0.018	−1.73
1370148_at	Hp	A>T	−3293	Pbx1	1.50E-03	1.50E-01	0.01	−1.99
1370065_at	Hpx	A>G	−4986	Oct1	7.20E-03	1.30E-01	0.058	−1.24
1370401_at	Ly6b	A>G	−4396	Atf4	3.60E-01	8.70E-03	41.3	1.62
1370401_at	Ly6b	T>C	−3505	Sry	1.40E-03	4.00E-05	36.3	1.56
1370401_at	Ly6b	T>C	−3505	Creb	6.70E-02	1.90E-03	35.8	1.55
1370401_at	Ly6b	A>G	−2224	E4F1	2.20E-01	7.90E-03	27.3	1.44
1370401_at	Ly6b	A>G	−2224	Crebp1	3.10E-02	1.20E-03	25.7	1.41
1370401_at	Ly6b	A>G	−2224	Creb	9.80E-02	4.20E-03	23	1.36
1370401_at	Ly6b	G>A	−3866	Hnf4a	5.50E-02	3.20E-03	17.4	1.24
1370401_at	Ly6b	A>G	−2224	Barbie	7.60E-03	2.40E-01	0.031	−1.50
1370401_at	Ly6b	A>C	−1048	Titf1	3.80E-03	2.30E-01	0.016	−1.78
1389572_at	Me3	T>A	−3512	Nkx3A	4.20E-02	2.20E-03	18.8	1.27
1372923_at	Pex11b	G>A	−554	Rfx	3.80E-01	4.00E-03	97	1.99
1370881_at	Tst	T>C	−3925	E2F1	2.50E-01	8.70E-03	28.7	1.46
1370881_at	Tst	T>C	−580	Cp2	1.50E-02	6.40E-04	23.9	1.38
1370881_at	Tst	C>A	−1907	AP2rep	5.80E-02	2.80E-03	20.7	1.32
1370881_at	Tst	T>C	−1192	CACCC binding factor	1.10E-01	5.90E-03	17.9	1.25
1370881_at	Tst	T>C	−1192	Cdpcr3	8.4E-03	1.5E-01	0.055	−1.26
1370881_at	Tst	T>A	−161	AP2rep	3.2E-04	8.2E-03	0.039	−1.41

^aSingle nucleotide polymorphism (SNP) observed in SHR compared with BN reference sequence.

^bDistance of SNP from transcription start site (TSS) in Ensembl (http://www.ensembl.org/Rattus-norvegicus/Info/Index).

^cNormalized measure of binding affinity of the transcription factor to the putative site in BN.

^dNormalized measure of binding affinity of the transcription factor to the putative site in SHR.

^eThe ratio of binding affinity of the transcription factor between the strains (BN/SHR).

^fLog₁₀ transformed ratio (BN/SHR).