Table 7.

Comparison of GWAS results of our phenotype of interest when a) not adjusting for principal components, b) adjusting for the first three principal components and c) adjusting for the first three principal components and APOE status

Top 20 SNPs for GWAS w/o PCs			Top 20 SNPs for GWAS with PC1, PC2 & PC3			Top 20 SNPs for GWAS with PC1, PC2, PC3 and APOE
CHR	SNP	p-value	CHR	SNP	p-value	CHR	SNP	p-value
14	rs3748348	1.92×10−7	14	rs3748348	2.12e-07	14	rs3748348	2.13×10−7
2	rs1609361	1.96×10−6	2	rs1609361	2.099e-06	2	rs1609361	2.15×10−6
10	rs7897741	5.03×10−6	10	rs7897741	5.907e-06	10	rs7897741	6.04×10−6
8	rs13251704	9.10×10−6	2	rs16987794	1.103e-05	2	rs16987794	1.12×10−5
2	rs2698011	1.16×10−5	8	rs13251704	1.163e-05	8	rs13251704	1.18×10−5
2	rs2698029	1.26×10−5	2	rs2698011	1.294e-05	2	rs2698011	1.31×10−5
2	rs2715077	1.26×10−5	2	rs2715077	1.366e-05	12	rs7306879	1.39×10−5
2	rs16987794	1.38×10−5	12	rs7306879	1.422e-05	2	rs2715077	1.40×10−5
12	rs7306879	2.10×10−5	2	rs2698029	1.438e-05	2	rs2698029	1.48×10−5
4	rs4865353	2.13×10−5	4	rs4865353	2.23e-05	4	rs4865353	2.28×10−5
8	rs13258868	2.75×10−5	14	rs2365682	2.585e-05	14	rs2365682	2.63×10−5
14	rs2365682	2.77×10−5	12	rs11055126	3.007e-05	12	rs11055126	3.06×10−5
2	rs2698024	3.39×10−5	8	rs13258868	3.1e-05	8	rs13258868	3.15×10−5
12	rs11055126	3.50×10−5	5	rs13183341	3.412e-05	5	rs13183341	3.48×10−5
3	rs9851461	3.65×10−5	6	rs9344230	3.519e-05	6	rs9344230	3.49×10−5
15	rs4456480	3.66×10−5	12	rs12316661	3.754e-05	6	rs1737038	3.79×10−5
12	rs12316661	3.94×10−5	6	rs1737038	3.756e-05	12	rs12316661	3.81×10−5
3	rs6809436	3.98×10−5	2	rs2698024	3.81e-05	2	rs2698024	3.89×10−5
6	rs1737038	4.02×10−5	3	rs9851461	4.16e-05	15	rs4456480	4.05×10−5
6	rs9344230	4.03×10−5	15	rs4456480	4.186e-05	3	rs9851461	4.08×10−5

PC Principal component