Table 6.

Candidate SNP markers near TBP-binding sites within promoters of the human genes associated with familial AD.

Gene (OMIM ID)	dbSNP rel. 147 or see (Ref)	5′ flank	wt mut	3′ flank	K D , nM					Hypothetical disease, which could be associated with a candidate SNP marker (Figure S1: Supplementary File 2)	References
					wt mut	Δ	Z	α	ρ
MAPT (157140)	rs374878846	accttctgcc	g a	ccgccaccac	61 55	↑	2	0.05	D	(hypothetically) higher risks of AD, neuroinflammation in AD; neuronal loss	(this work), Wirths and Bayer, 2010; Saman et al., 2014; Wes et al., 2014
	rs553179073	ccgctgccac	c t	gcccaccttc	61 68	↓	2	0.05	D	(hypothetically) higher survival in AD, prevention of memory deficits and neuroprotective effects but can be involved in long-term depression and frontotemporal degeneration	(this work), Ittner et al., 2010; Maphis et al., 2015; Papegaey et al., 2016
	rs11872014	acactcctca	g a	aacttatcct	10 13	↓	2	0.05	D
APP (104760)	rs200621906	ggggtgggcc	g a	gatcagctga	91 56	↑	10	10−6	A	(hypothetically) higher risk of AD (seven-fold APP-overexpressing mice of the APP23 strain are one of the widely accepted murine models of AD)	(this work), Sturchler-Pierrat et al., 1997
	rs536423638	cgggctccgt	c t	agtttcctcg	68 24	↑	19	10−6	A
	rs558863815	gactcgcctg	g a	ctctgagccc	109 91	↑	4	10−3	B
	rs759517529	actggctgaa	g a	aaagtgacaa	36 30	↑	4	10−3	B
	rs756747509	ccctgcctca	a g	gtaacaattg	10 12	↓	3	10−3	B	(hypothetically) higher risk of cognitive deficits without AD-like anatomical changes (APP−/− mice)	(this work), Zhang et al., 2016
	rs561135968	aagaaaatcc	t a	acaaaaggaa	6 10	↓	7	10−6	A
APOE (107741)	rs762555354	cccacctcg	g t	actgggggct	58 21	↑	15	10−6	A	(hypothetically) lower risk of AD via reduced growth of Aβ plaques	(this work), Bien-Ly et al., 2012
	rs758661090	gcgagactgg	g c	actgagatgg	54 48	↑	2	0.05	D
	rs769448	gagatggaac	g c	ggcggtgggg	54 46	↑	3	10−2	C
	rs758379972	ggggagccct	a g	taattggaca	5 16	↓	16	10−6	A	(hypothetically) higher risk of AD via Aβ accumulation	(this work), Ohman et al., 1996
PSEN1 (104311)	rs201362083	ctcccctcct	c t	cgtgggccgg	107 58	↑	13	10−6	A	(hypothetically) higher risk of AD via death of postmitotic neurons after injury, but lower risk of AD due to an anti-apoptotic protective effect in neurons after apoptosis induction	(this work), Vezina et al., 1999; Prat et al., 2002
	rs202209472	ggccgccaac	g a	acgccagagc	107 55	↑	13	10−6	A
	rs1800839	ccgccaacga	c t	gccagagccg	107 72	↑	8	10−6	A
	rs199959804	ggtggagaga	g a	attccgggga	51 35	↑	7	10−6	A
	rs563558461	ggccccgccc	c t	cttcctcctg	96 78	↑	4	10−3	B
	rs752158054	accaggaggg	25 bp −	gcggccgggt	51 83	↓	9	10−6	A	(hypothetically) higher risk of AD with age-dependent onset (double knockout PSEN1−/−PSEN2−/− murine model), but lower risk of AD due to PSEN1-deficiency inhibits Aβ-plaque formation and corrects hippocampal long-term potentiation	(this work), Dewachter et al., 2002; Aoki et al., 2009
	rs530970418	gccccgcccc	c g	ttcctcctgg	96 78	↓	4	10−3	B
	rs772984560	aaacagtatt	t c	ctatacagtt	3 6	↓	7	10−6	A
	rs796710298	gtatttctat	t c	cagttgctcc	3 6	↓	10	10−6	A
PSEN2 (600759)	rs761796296	tgtttcattt	c t	gtgtgtgttg	11 9	↑	6	10−6	A	(hypothetically) higher risk of AD	(this work), Gamliel et al., 2002
	rs556146702	cgtggcctgg	g t	cgggcgtggg	352 220	↑	9	10−6	A
	rs544497401	cccagtggac	g a	agggaacgcg	81 41	↑	11	10−6	A
	rs758016212	ggggccccag	t c	ggacgaggga	81 117	↓	6	10−6	A	(hypothetically) higher risk of AD with age-dependent emergence (double PSEN1−/−PSEN2−/−mice); AD-like neurodegeneration and lung tumor development (PSEN2−/−mice); age-dependent hemorrhage and pulmonary fibrosis (PSEN1+/−PSEN2−/−mice)	(this work), Herreman et al., 1999; Chen et al., 2008; Aoki et al., 2009; Yun et al., 2014
	rs564994558	gggccccagt	- g	ggacgaggga	81 102	↓	4	10−3	B
	rs201944966	agagccggtt	t c	ctgttagcag	25 32	↓	4	10−3	B