Candidate SNP markers of reproductive potential are predicted by a significant change in the affinity of TATA-binding protein for human gene promoters

Chadaeva, Irina V.; Ponomarenko, Petr M.; Rasskazov, Dmitry A.; Sharypova, Ekaterina B.; Kashina, Elena V.; Zhechev, Dmitry A.; Drachkova, Irina A.; Arkova, Olga V.; Savinkova, Ludmila K.; Ponomarenko, Mikhail P.; Kolchanov, Nikolay A.; Osadchuk, Ludmila V.; Osadchuk, Alexandr V.

doi:10.1186/s12864-018-4478-3

Table 2 Known and candidate SNP markers of tumors in nonreproductive organs

From: Candidate SNP markers of reproductive potential are predicted by a significant change in the affinity of TATA-binding protein for human gene promoters

Gene	dbSNP [6] rel. 147 or see [Ref]	5′ flank	wt mut	3′ flank	K_D, nM					Known diseases (SNP markers) or hypothetical disease (candidate SNP markers)	[Ref] or [this work]
Gene	dbSNP [6] rel. 147 or see [Ref]	5′ flank	wt mut	3′ flank	wt mut	Δ	Z	α	ρ		[Ref] or [this work]
IL1B	rs1143627	ttttgaaagc	c t	ataaaaacag	5 2	↑	15	10^-6	A	high risks of gastric, liver, and non–small cell lung cancers; gastric ulcer, chronic gastritis, recurrent major depression, obesity, Graves’ disease, pre-eclampsia, (hypothetically) short time-to-delivery in pregnancy and childbirth	[77,78,79,80,81,82,83,84,85] [this work]
IL1B	rs549858786	tgaaagccat	a t	aaaacagcga	5 7	↓	8	10^-6	A	(hypothetically) lesser risk of the same diseases	[60]
CYP2A6	rs28399433	tcaggcagta	t g	aaaggcaaac	2 9	↓	21	10^-6	A	low risk of lung cancer in smokers (LUC: “-34g” corresponds to 50% of “-34t”), (hypothetically) lesser damage from secondhand smoke in pregnant women who are nonsmokers	[86, 87], [this work], [90,91,92]
CYP2A6	rs761592914	tttttcaggc	a c	gtataaaggc	2 3	↓	3	10^-3	B	(hypothetically) the same disease	[this work]
CYP2B6	rs34223104	gatgaaattt	t c	ataacagggt	4 10	↓	15	10^-6	A	TATA_WT→USF_SNP, TSS_WT→TATA_SNP, and de-novo TSS_SNP can cause overexpression of this gene of a bioactivator of immunosuppressive and antitumor prodrug cyclophosphamide	[88]
CYP2B6	rs563558831	tgaaatttta	t c	aacagggtgc	4 10	↓	13	10^-6	A	(hypothetically) the same problem	[this work]
DHFR	rs10168	ctgcacaaat	g a	gggacgaggg	15 9	↑	9	10^-6	A	resistance to methotrexate treatment of leukemia and (hypothetically) that in the cases of ectopic pregnancy, metastatic choriocarcinoma, and gestational trophoblastic disease	[89], [this work], [93]
	rs750793297	tgcacaaatg	g t	ggacgagggg	15 13	↑	3	10^-2	C	(hypothetically) the same diseases	[this work]
	rs766799008	ctgcacaaat	a g	tggggacgag	15 19	↓	3	10^-3	B	(hypothetically) greater bioactivity of methotrexate during treatment of leukemia, ectopic pregnancy, metastatic choriocarcinoma, and gestational trophoblastic disease	[this work], [60]
	rs764508464	ctgcacaaat	a -	tggggacgag	15 37	↓	17	10^-6	A
	rs754122321	ctcgcctgca	c g	aaatggggac	15 25	↓	9	10^-3	B

See “Note” under Table 1

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ISSN: 1471-2164

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