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 7 Candidate SNP markers of reproductivity-related genes

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					hypothetical disease (candidate SNP markers)	[this work], [Ref]
Gene	dbSNP [6] rel. 147 or see [Ref]	5′ flank	wt mut	3′ flank	wt mut	Δ	Z	α	ρ	hypothetical disease (candidate SNP markers)	[this work], [Ref]
AR	rs763353257	aagggaagta	g -	gtggaagatt	30 21	↑	6	10^-6	A	(hypothetically) higher risks of androgenetic alopecia and androgen-induced premature senescence in adult men	[251]
	rs749306567	aagggaagta	g a	gtggaagatt	30 15	↑	11	10^-6	A
	rs377711437	cagcactgca	g a	ccacgacccg	75 66	↑	2	0.05	D
MTHFR	rs780207553	cacgcactct	g a	ggcctgagct	74 38	↑	12	10^-6	A	(hypothetically) higher risk of pre-eclampsia	[252]
	rs749532075	tccctcccca	c t^*)	gcactctggg	74 50	↑	7	10^-6	A
	rs771960561	cctctgttcc	c t	tccccacgca	74 66	↑	3	10^-2	B
	rs773214376	tgcctctgtt	c t	cctccccacg	74 66	↑	2	0.05	D
	rs566478202	ggtgcctctg	t g	tccctcccca	74 85	↓	2	0.05	D	(hypothetically) higher risk of adverse pregnancy outcomes	[253]
	rs752181249	gaggatctac	a c	gccatcagct	27 35	↓	4	10^-3	B		[253]
DNMT1	rs570287204	gtgggggggg	- gtg	tgtgtgcccg	52 23	↑	11	10^-6	A	(hypothetically) under stress, higher risk of epigenetic disorders of fetal and newborn brain development causing long-term neurobehavioral problems that may be reversible in adolescence	[254, 255]
	rs534819409	cgtggggggg	g t	ggcctgagct	52 30	↑	7	10^-6	A
	rs553454792	gcgtgggggg	g t	gtgtgtgccc	52 23	↑	11	10^-6	A
	rs558447661	cgtggagctt	g t	gacgagccca	72 29	↑	15	10^-6	A
	rs535899986	cccagcaaac	c t	gtggagcttg	72 58	↑	5	10^-3	B
	rs143796354	cacctcccag	c a	aaaccgtgga	72 26	↑	20	10^-6	A
	rs756103340	gcggcgcgca	g a	cggcagttgg	92 79	↑	3	10^-3	B
	rs758026532	ccagcaaacc	g t^*)	tggagcttgg	72 88	↓	4	10^-3	B	(hypothetically) higher risks of activation of protooncogenes in cancer	[256]
	rs772821225	gtctccaata	a c	atgcagctgg	7 8	↓	2	0.05	D		[256]
CYP17A1	rs758657961	ctggagttga	g a	ccagcccttg	56 30	↑	11	10^-6	A	(hypothetically) higher risk of hyperandrogenism in polycystic ovary syndrome	[257]
CYP17A1	rs373488849	tgccctggag	t c	tgagccagcc	56 70	↓	4	10^-3	B	(hypothetically) higher risk of fertility impairments	[258]
NR5A1	rs147497093	gttcagcaag	c t	acaagagaaa	19 6	↑	17	10^-6	A	(hypothetically) higher risks of adrenal tumors and endometriosis	[259]
	rs535432539	cgctgcttcc	g a	cttcgtaagt	31 18	↑	9	10^-6	A
	rs553326158	gcgctgcttc	c t	gcttcgtaag	31 26	↑	3	10^-2	C
	rs143242438	caccctcatc	c t	ggtgtgagag	31 21	↑	6	10^-6	A

See the footnote of Table 1; ^*)this SNP includes one more minor neutral allele: “a.”

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ISSN: 1471-2164

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