Behavioural Neurology

Research Article

Use of Deep-Learning Genomics to Discriminate Healthy Individuals from Those with Alzheimer’s Disease or Mild Cognitive Impairment

Table 4

Shared significant SNPs in AD multitasking classification at threshold of 0.05.


SNP loci	Chr	Position	Region or closest gene	Major/minor alleles	value HC vs. AD	value HC vs. MCI	value AD vs. MCI

rs12091371	1	238671675	FMN2	A/G	0.002227833	0.001509792	2.27881-09
rs12129547	1	238761878	GREM2	T/C	0.002767757	0.019531535	3.93396-11
rs1801131	1	11777063	MTHFR	C/A	0.000154746	0.007333869	6.18756-21
rs1801133	1	11778965	MTHFR	T/C	0.000192989	0.009566143	5.35043-21
rs17034806	2	109002337	RANBP2	G/A	0.002645921	0.028425309	3.04207-10
rs243034	2	60456396	MIR4432HG	G/A	0.038985718	0.009492742	1.40355-08
rs4676049	2	109001689	RANBP2	T/C	0.002215778	0.034993277	4.51555-10
rs6714710	2	97711518	ZAP70	G/T	0.038909198	0.000768783	7.036-09
rs1498853	3	69691797	NAN^a	G/A	0.000708166	0.012435495	6.43721-09
rs2289506	3	101547592	NIT2	T/C	0.000412705	0.004914541	1.07429-18
rs288496	3	69714739	NAN^a	T/C	0.002172998	0.009409715	4.5892-09
rs3864101	3	188862449	NAN^a	T/G	0.038241862	0.022506051	6.17468-08
rs989692	3	156284059	MME	T/C	0.00243336	0.016131413	5.91293-09
rs3796529	4	57492171	REST	A/G	0.048696066	0.004826601	7.08294-25
rs753129	4	56363188	NAN^a	C/T	0.004469287	1.23015-10	0.013855564
rs1925458	6	23486930	LOC102724749; LOC105374976	T/G	0.000567167	0.000409483	3.10404-11
rs1980493	6	32471193	BTNL2; TSBP1-AS1	G/A	0.016858811	0.000751139	3.35304-14
rs2651206	6	43321455	TTBK1	T/C	0.034368574	2.23746-07	1.97506-11
rs3734254	6	35502988	PPARD	C/T	0.001667544	0.000173601	2.21574-11
rs3747742	6	41270496	TREML2	C/T	6.7184-06	3.50103-05	1.19671-08
rs6455128	6	62755705	KHDRBS2	A/C	0.008767325	0.00013524	1.45915-14
rs11767557	7	142819261	EPHA1-AS1	C/T	0.001139233	1.20661-07	1.96401-07
rs11771145	7	142820884	EPHA1-AS1	A/G	0.001112928	9.62693-08	1.8557-07
rs2227631	7	100556258	SERPINE1	G/A	0.003024669	8.25065-08	7.24385-07
rs6461569	7	21502301	SP4	C/T	0.025204688	1.41338-06	0.001322394
rs6966915	7	12232513	TMEM106B	T/C	0.031810788	0.004328052	6.57464-09
rs11136000	8	27520436	CLU	T/C	0.000663408	8.36729-06	1.48921-07
rs1975804	8	109360409	EIF3E; LOC105375704	C/T	0.000833268	0.003779274	0.040135088
rs1800977	9	106730271	ABCA1; LOC105376196	T/C	0.013227434	5.61278-05	4.22923-14
rs2007153	9	135493640	DBH	A/G	3.88584-05	0.000993637	4.15766-07
rs2066715	9	106627854	ABCA1	A/G	0.004157538	0.04271672	7.79217-05
rs2283123	9	135505118	DBH	T/C	0.000105332	0.00221966	1.99182-07
rs2740483	9	106730356	ABCA1; LOC105376196	C/G	0.009678488	6.53287-05	3.81638-14
rs4149313	9	106626574	ABCA1	G/A	0.003318514	0.040059489	7.22211-05
rs4878104	9	89382811	DAPK1	T/C	0.002309724	6.11706-05	1.46237-14
rs4548513	10	67710331	CTNNA3	T/C	0.004692221	0.000992064	6.62732-08
rs7070570	10	67534610	LOC105378340; CTNNA3	G/A	0.000655491	2.34147-05	1.63609-06
rs10501602	11	85359037	PICALM	G/A	0.004647595	3.42511-08	2.27238-13
rs1133174	11	121006965	SORL1	A/G	0.010544659	0.003255318	3.13279-05
rs12805520	11	85308059	CCDC83	T/C	0.007162755	4.02484-08	1.90295-11
rs1354269	11	19330820	NAV2	C/T	0.010833795	6.42781-08	2.65216-24
rs1695	11	67109265	GSTP1	G/A	0.006309008	6.1645-07	2.06528-23
rs1699102	11	120962172	SORL1	C/T	0.013141699	0.001477832	6.19383-05
rs17571	11	1739170	CTSD	T/C	0.013910348	1.48442-08	1.58542-20
rs1946518	11	111540668	IL18	T/G	0.006486007	1.8075-06	7.21291-22
rs2070045	11	120953300	SORL1	G/T	0.014545915	0.001140944	7.97485-05
rs3851179	11	85546288	PICALM	A/G	0.00599555	1.06305-06	1.50773-20
rs543293	11	85497725	PICALM	A/G	0.004782682	1.26328-07	7.85454-18
rs6265	11	27636492	BDNF; BDNF-AS	A/G	0.009460455	1.96067-07	1.42052-28
rs7120118	11	47242866	NR1H3	C/T	0.034010947	0.011720707	5.90652-22
rs7943454	11	24478242	LUZP2	T/C	0.01777448	1.41141-06	2.00064-30
rs1799986	12	55821533	LRP1	T/C	0.000875404	8.1991-06	0.000948497
rs6311	13	46369479	HTR2A	T/C	1.95644-05	0.002519461	1.48261-11
rs6313	13	46367941	HTR2A	T/C	3.21121-05	0.004551786	2.05426-12
rs690705	13	33552918	RFC3	G/A	9.15016-07	0.000123939	0.032894005
rs7989332	13	19948575	CRYL1	A/C	0.001947338	0.038324875	0.017831896
rs10137185	14	63845529	ESR2	T/C	0.000105484	0.00099597	2.08051-22
rs1065778	15	49307498	MIR4713HG; CYP19A1	A/G	7.88465-05	1.51664-05	2.28151-18
rs2278317	15	31848032	RYR3	G/A	0.019133823	5.18518-05	4.11594-07
rs3751592	15	49393870	CYP19A1; MIR7973-1; MIR7973-2	G/A	0.000333452	8.25536-05	5.77922-13
rs11075996	16	52415525	FTO	T/C	0.021538201	9.92354-07	0.002856803
rs11075997	16	52416413	FTO	T/C	0.023256237	1.14854-06	0.002461173
rs6499640	16	52327178	FTO	G/A	0.016928027	4.22569-07	0.009148135
rs1050565	17	25600202	BLMH	G/A	0.045066195	6.1136-06	1.19122-06
rs391300	17	2163008	SRR	A/G	0.028223591	1.90848-06	0.000379785
rs7946	17	17350285	PEMT	C/T	0.044709718	0.000412862	2.75631-18

SNP: single-nucleotide polymorphism. Chr: chromosome. NAN^a represents uncertain gene of the SNP loci. value (HC vs. AD) represents the difference value of each SNP loci between AD and HC groups. All value are calculated by a two-sample test for false discovery rate correction.