Genome-wide association reveals genetic effects on human Aβ 42 and τ protein levels in cerebrospinal fluids: a case control study

Han, Mi-Ryung; Schellenberg, Gerard D; Wang, Li-San

doi:10.1186/1471-2377-10-90

Table 3 Linear regression result for SNPs with CSF biomarkers in Normal, MCI and AD subjects (Top SNPs with p-value < 10^-6)

From: Genome-wide association reveals genetic effects on human Aβ ₄₂ and τ protein levels in cerebrospinal fluids: a case control study

Linear regression result without using covariates
Normal: Aβ_1-42
Chromosome	SNP	Position	A1	TEST	BETA	STAT	P-value	Gene Symbol, Gene Name
15	rs2899472	49303347	A	GENO_2DF	NA	40.21	1.86E-09	CYP19A1, cytochrome p450, family 19, subfamily a, polypeptide 1
15	rs2899472	49303347	A	DOMDEV	0.1791	5.859	5.40E-08	CYP19A1, cytochrome p450, family 19, subfamily a, polypeptide 1
1	rs11206801	56623274	A	GENO_2DF	NA	33.14	6.37E-08
1	rs4431886	56624855	C	GENO_2DF	NA	33.14	6.37E-08
15	rs2899472	49303347	A	ADD	-0.1407	-5.699	1.11E-07	CYP19A1, cytochrome p450, family 19, subfamily a, polypeptide 1
19	rs2075650	50087459	G	GENO_2DF	NA	30.02	3.03E-07	TOMM40, translocase of outer mitochondrial membrane 40 homolog (yeast)
12	rs10784496	64447238	G	GENO_2DF	NA	29.98	3.09E-07
7	rs12534221	130938530	A	GENO_2DF	NA	27.83	9.04E-07
6	rs1727638	72196293	A	GENO_2DF	NA	27.69	9.71E-07
Normal: T-tau
Chromosome	SNP	Position	A1	TEST	BETA	STAT	P-value	Gene Symbol, Gene Name
12	rs1997111	117872301	T	GENO_2DF	NA	36.66	1.10E-08
12	rs11069178	117852210	C	GENO_2DF	NA	31.23	1.65E-07
2	rs17189298	119561787	A	GENO_2DF	NA	29.51	3.90E-07
8	rs2935776	109699079	C	GENO_2DF	NA	28.81	5.53E-07
8	rs2928826	109683270	T	GENO_2DF	NA	28.73	5.77E-07
2	rs895401	119584178	G	GENO_2DF	NA	27.86	8.90E-07
2	rs893769	119556554	C	ADD	-0.1024	-5.237	8.92E-07
Normal: P-tau _181p
Chromosome	SNP	Position	A1	TEST	BETA	STAT	P-value	Gene Symbol, Gene Name
18	rs1943816	69209602	C	GENO_2DF	NA	32.09	1.08E-07
2	rs2074955	158686040	C	GENO_2DF	NA	32.06	1.09E-07	UPP2, uridine phosphorylase 2
MCI: T-tau
Chromosome	SNP	Position	A1	TEST	BETA	STAT	P-value	Gene Symbol, Gene Name
22	rs5998432	31075916	T	GENO_2DF	NA	27.91	8.696E-07
MCI: P-tau _181p
Chromosome	SNP	Position	A1	TEST	BETA	STAT	P-value	Gene Symbol, Gene Name
2	rs7558386	227270383	G	GENO_2DF	NA	32.09	1.08E-07
2	rs7558386	227270383	G	DOMDEV	0.242	5.343	5.27E-07
3	rs7631605	37209593	T	GENO_2DF	NA	27.71	9.60E-07
AD: Aβ _1-42
Chromosome	SNP	Position	A1	TEST	BETA	STAT	P-value	Gene Symbol, Gene Name
21	rs239713	27618347	T	GENO_2DF	NA	29.03	4.96E-07
AD: T-tau
Chromosome	SNP	Position	A1	TEST	BETA	STAT	P-value	Gene Symbol, Gene Name
20	rs4925189	59380439	G	DOMDEV	0.1969	5.178	6.35E-07	CDH4, cadherin 4, type 1, R-cadherin (retinal)
AD: P-tau _181p
Chromosome	SNP	Position	A1	TEST	BETA	STAT	P-value	Gene Symbol, Gene Name
4	rs12643654	96378840	G	GENO_2DF	NA	29.04	4.95E-07	UNC5C, unc-5 homolog C (C. elegans)
Linear regression result using APOE genotype and age as covariates
Normal: Aβ _1-42
Chromosome	SNP	Position	A1	TEST	BETA	STAT	P-value	Gene Symbol, Gene Name
15	rs2899472	49303347	A	GENO_2DF	NA	53.98	1.90E-12	CYP19A1, cytochrome p450, family 19, subfamily a, polypeptide 1
15	rs2899472	49303347	A	ADD	-0.1393	-6.925	3.85E- 0	CYP19A1, cytochrome p450, family 19, subfamily a, polypeptide 1
15	rs2899472	49303347	A	DOMDEV	0.1614	6.425	4.15E-09	CYP19A1, cytochrome p450, family 19, subfamily a, polypeptide 1
21	rs1022442	21277717	A	GENO_2DF	NA	30.21	2.75E-07	NCAM2, neural cell adhesion molecule 2
10	rs2493624	19102262	G	GENO_2DF	NA	28.61	6.14E-07
10	rs11015839	19042893	A	GENO_2DF	NA	28.51	6.45E-07	ARL5B, adp-ribosylation factor-like 5b
10	rs11015860	19045045	G	GENO_2DF	NA	28.51	6.45E-07
1	rs10911736	183689227	A	GENO_2DF	NA	28.16	7.69E-07
10	rs11015839	19042893	A	ADD	-0.1151	-5.257	7.87E-07
10	rs11015860	19045045	G	ADD	-0.1151	-5.257	7.87E-07
10	rs11015939	19057948	A	ADD	-0.1243	-5.219	9.25E-07
10	rs2495832	19114467	G	ADD	-0.1243	-5.219	9.25E-07
6	rs12203791	67778209	T	GENO_2DF	NA	27.68	9.76E-07
10	rs10763625	19074957	T	ADD	-0.124	-5.206	9.78E-07
Normal: T-tau
Chromosome	SNP	Position	A1	TEST	BETA	STAT	P-value	Gene Symbol, Gene Name
12	rs1997111	117872301	T	GENO_2DF	NA	30.74	2.11E-07
2	rs17189298	119561787	A	GENO_2DF	NA	27.92	8.66E-07
18	rs1021599	28469054	T	GENO_2DF	NA	27.88	8.81E-07
Normal: P-tau _181p
Chromosome	SNP	Position	A1	TEST	BETA	STAT	P-value	Gene Symbol, Gene Name
18	rs1943816	69209602	C	GENO_2DF	NA	31.43	1.50E-07
2	rs2074955	158686040	C	GENO_2DF	NA	30.78	2.07E-07	UPP2, uridine phosphorylase 2
MCI: Aβ _1-42
Chromosome	SNP	Position	A1	TEST	BETA	STAT	P-value	Gene Symbol, Gene Name
10	rs2986971	30136634	G	GENO_2DF	NA	31.88	1.20E-07
10	rs2986971	30136634	G	ADD	0.08328	5.228	8.88E-07
MCI: T-tau
Chromosome	SNP	Position	A1	TEST	BETA	STAT	P-value	Gene Symbol, Gene Name
4	rs2768975	48724658	G	GENO_2DF	NA	30.89	1.96E-07	FLJ21511, hypothetical protein flj21511
4	rs6850199	48695607	A	GENO_2DF	NA	29.93	3.18E-07	FLJ21511, hypothetical protein flj21511
18	rs1445093	48024821	C	GENO_2DF	NA	28.14	7.75E-07
MCI: P-tau _181p
Chromosome	SNP	Position	A1	TEST	BETA	STAT	P-value	Gene Symbol, Gene Name
7	rs121724	29207970	G	GENO_2DF	NA	31.49	1.45E-07	CHN2, chimerin (chimaerin) 2
8	rs7842088	17629409	G	GENO_2DF	NA	30.73	2.12E-07	MTUS1, mitochondrial tumor suppressor 1

Abbreviations: SNP, single-nucleotide polymorphism; ADD, additive effects of allele dosage; DOMDEV, dominance deviation from additivity, rather specifying that a particular allele is dominant or recessive; GENO_2DF, a 2 df joint test of both additive and dominance; A1, tested allele (minor allele); BETA, regression coefficient; STAT, coefficient t-statistic

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ISSN: 1471-2377

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