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 3 Known and candidate reproductivity-related SNP markers in genes of hormones

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]
LEP	rs201381696	tcgggccgct	a g	taagaggggc	4 12	↓	17	10^-6	A	hypoleptinemia elevates risk of obesity	[54, 106]
	rs200487063	tgatcgggcc	g a	ctataagagg	4 2	↑	6	10^-6	A	(hypothetically) hyperleptinemia elevates risk of hypertension in obesity	[this work], [107, 110]
	rs34104384	ccgctataag	a t	ggggcgggca	4 3	↑	4	10^-2	C		[this work], [107, 110]
GCG	rs183433761	gctggagagt	a g	tataaaagca	0.9 1.6	↓	17	10^-6	A	resistance to obesity during a high-fat diet	[54]
	rs183433761	gctggagagt	a g	tataaaagca	0.9 1.6	↓	17	10^-6	A	(hypothetically) hypoglucogonemia decreases pregnancy probability, serum insulin in pregnancy, and during late gestational period	[this work], [111, 112]
	rs757035851	tatataaaag	cag -	tgcgccttgg	0.9 1.1	↓	3	10^-3	B		[this work], [111, 112]
GH1	rs11568827	aggggccagg	g -	tataaaaagg	1.5 1.4	=	1	1	E	short stature (EMSA: unknown TF-binding site lost, not TATA box)	[107]
	rs11568827	aggggccagg	g -	tataaaaagg						(hypothetically) higher risk of GH1 deficiency as clinical syndrome whose symptoms are increased central adiposity, atherogenesis, as well as cerebrovascular and cardiac morbidity (and mortality), and, also, decreased lean body mass, bone mineral density, quality of life	[this work], [113]
	rs796237787	gaaggggcca	g -	ggtataaaaa
	rs768454929	agggtataaa	a c	agggcccaca	1.5 2.6	↓	7	10^-6	A
	rs761695685	gccagggtat	a g	aaaagggccc	1.5 5.8	↓	19	10^-6	A
	rs774326004	ccagggtata	a t	aaagggccca	1.5 0.9	↑	7	10^-6	A	(hypothetically) higher risks of acromegaly	[this work], [114]
	rs777003420	aaggggccag	g t	gtataaaaag	1.5 1.3	↑	3	0.05	D	(hypothetically) higher risks of acromegaly	[this work], [114]
INS	rs5505	agatcactgt	c t	cttctgccat	53 44	↑	4	10^-3	B	type 1 diabetes after neonatal diabetes mellitus	[108]
	rs5505	agatcactgt	c t	cttctgccat	53 44	↑	4	10^-3	B	(hypothetically) hyperinsulinemia elevates the placental leptin which causes neonatal macrosomia	[this work], [115]
	rs563207167	tcagccctgc	c t	tgtctcccag	53 44	↑	4	10^-3	B		[this work], [115]
	rs11557611	gatcactgtc	c t	ttctgccatg	53 60	↓	2	0.05	D	(hypothetically) hypoinsulinemia slows down fetal growth	[this work], [116]

See “Note” under Table 1

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ISSN: 1471-2164

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