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 5 Known and candidate reproductivity-related SNP markers related to blood proteins

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]
HBB	rs397509430	gggctgggca	t -	atacaacagt	5 29	↓	34	10^-6	A	malaria resistance and thalassemia	[176]
	rs33980857	gggctgggca	t a,g,c	atacaacagt	5 21	↓	27	10^-6	A
	rs34598529	ggctgggcat	a g	aaagtcaggg	5 18	↓	24	10^-6	A
	rs33931746	gctgggcata	a g,c	aagtcagggc	5 11	↓	14	10^-6	A
	rs33981098	agggctgggc	a g,c	taaaagtcag	5 9	↓	10	10^-6	A
	rs34500389	cagggctggg	c a,t,g	ataaaagtca	5 6	↓	3	10^-2	C
	rs34500389	cagggctggg	c a,t,g	ataaaagtca	5 6	↓	3	10^-2	C	(hypothetically) the same disease; heterozygotes “wt-mut” are still more viable according to most of clinical indicators in comparison with both homozygotes “wt-wt” and “mut-mut”	[this work], [185]
	rs63750953	ctgggcataa	aa -	gtcagggcag	5 8	↓	9	10 ^-6	A
	rs281864525	tgggcataaa	a c	gtcagggcag	5 7	↓	7	10 ^-6	A
	rs117785782	ggctgagggt	t c	tgaagtccaa	28 39	↓	7	10 ^-6	A
HBD	rs35518301	caggaccagc	a g	taaaaggcag	4 8	↓	11	10^-6	A	malaria resistance and thalassemia	[176]
	rs35518301	caggaccagc	a g	taaaaggcag	4 8	↓	11	10^-6	A	(hypothetically) the same disease; heterozygotes “wt-mut” are still more viable according to most of clinical indicators	[this work], [185]
	rs34166473	aggaccagca	t c	aaaaggcagg	4 8	↓	18	10 ^-6	A
HBG2	rs745580140	ggagttgctc	ta -	cacaagctct	11 22	↓	10	10 ^-6	A
ACKR1	rs2814778	ttggctctta	t c	cttggaagca	10 12	↓	4	10^-3	B	low white-blood-cell count and resistance to malaria, (hypothetically) pre-eclampsia	[177, 178], [this work], [186]
MBL2	rs72661131	tctatttcta	t c	atagcctgca	2 4	↓	12	10^-6	A	variable immunedefici-ency, pre-eclampsia, stroke,	[190,191,192]
	rs72661131	tctatttcta	t c	atagcctgca	2 4	↓	12	10^-6	A	(hypothetically) the same disease; higher risks of recurrent vulvovaginal infections	[this work], [187]
	rs562962093	atctatttct	a g	tatagcctgc	2 5	↓	15	10^-6	A
	rs567653539	tttctatata	g a	cctgcaccca	2 1	↑	12	10^-6	A	(hypothetically) reduced risks of recurrent vulvovaginal infections
MMP12	rs2276109	gatatcaact	a g	tgagtcactc	11 14	↓	3	10^-2	C	lower risk of psoriasis, systemic sclerosis, asthma	[193,194,195]
	rs2276109	gatatcaact	a g	tgagtcactc	11 14	↓	3	10^-2	C	(hypothetically), higher risk of ovarian hyper-stimulation syndrome	[this work], [188]
	rs572527200	gatgatatca	a g	ctatgagtca	11 14	↓	3	10^-2	C		[this work], [188]
F2	rs564528021	agttcaacat	t c	aacccagagg	13 9	↑	7	10^-6	A	(hypothetically) high risk of pre-eclampsia	[this work], [189]
F2	rs752364393	caacattaac	c t	cagaggggtc	13 11	↑	3	10^-3	B	(hypothetically) high risk of pre-eclampsia	[this work], [189]

See “Note” under Table 1

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