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. Author manuscript; available in PMC: 2012 May 21.
Published in final edited form as: Arch Neurol. 2011 Dec;68(12):1569–1579. doi: 10.1001/archneurol.2011.646

Table 5.

Association of Alzheimer Disease With Genome-wide Significant Regions in White GWASs

Gene, SNP Effect Allele AFCEU Previously Reported Results in White Cohort
Results in African American Cohort
Source AF P Value OR (95% CI) AF P Value OR (95% CI)
CLU
 rs2279590 T 0.31 Lambert et al,19 2009 NR 9.2 × 10−8 0.87 (0.83–0.92) 0.12 .034 1.41a (1.03–1.95)
 rs11136000 T 0.35 Lambert et al,19 2009 NR 2.0 × 10−8 0.86 (0.82–0.91) graphic file with name nihms375246t1.jpg 0.56 .951 1.01 (0.84–1.20)
Seshadri et al,20 2010 0.39 1.62 × 10−16 0.85 (0.82–0.88)
Harold et al,21 2009 0.40 8.5 × 10−10 0.86 (0.82–0.90)
 rs9331888 G 0.32 Lambert et al,19 2009 NR 1.4 × 10−7 1.15 (1.09–1.22) 0.20 >.99 1.00 (0.76–1.32)
 rs9331926b G 0.07 . . . . . . . . . . . . 0.04 .020 1.96 (1.11–3.48)
PICALM
 rs3851179 T 0.41 Seshadri et al,20 2010 0.37 3.16 × 10−12 0.87 (0.84–0.91) graphic file with name nihms375246t2.jpg 0.16 .157 0.85 (0.68–1.07)
Harold et al,21 2009 0.37 1.3 × 10−9 0.86 (0.82–0.90)
 rs17148827c C 0.00 . . . . . . . . . . . . 0.04 .0089 2.01 (1.19–3.40)
 rs12795381d C 0.14 . . . . . . . . . . . . 0.04 .0086 0.49 (0.29–0.84)
CR1
 rs6656401 A 0.24 Lambert et al,19 2009 NR 7.9 × 10−9 1.20 (1.13–1.28) 0.07 .227 0.79 (0.54–1.16)
 rs3818361 A 0.26 Lambert et al,19 2009 NR 1.4 × 10−7 1.18 (1.11–1.25) 0.43 .466 0.94 (0.79–1.11)
BIN1
 rs744373 G 0.31 Seshadri et al,20 2010 0.29 1.59 × 10−11 1.15 (1.11–1.20) 0.48 .999 1.00 (0.84–1.20)
 rs11685593e T 0.21 . . . . . . . . . . . . 0.06 .0098 1.66 (1.13–2.45)
 rs11691237f T 0.27 . . . . . . . . . . . . 0.10 .0098 1.52 (1.11–2.09)
 rs7585314g T 0.85 . . . . . . . . . . . . 0.33 .0030 0.75 (0.62–0.91)
CD2AP
 rs9349407 C 0.28 Naj et al,22 2011 0.27 8.6 × 10−9 1.11 (1.07–1.15) 0.22 .854 0.98 (0.78–1.22)
EPHA1
 rs11767557 C 0.20 Naj et al,22 2011 0.19 6.0 × 10−10 0.90 (0.86–0.93) 0.18 .586 1.06 (0.86–1.31)
 rs11762262h T 0.20 . . . . . . . . . . . . 0.23 .034 1.27 (1.02–1.59)
 rs4595035i T 0.37 . . . . . . . . . . . . 0.43 .0094 1.25 (1.06–1.47)
MS4A
 rs4938933 C 0.50 Naj et al,22 2011 0.39 1.7 × 10−9 0.88 (0.85–0.92) 0.30 .493 1.06 (0.88–1.29)
 rs610932 T 0.54 Hollingworth et al,23 2011 . . . 1.8 × 10−14 0.90 (0.87–0.92) 0.49 .299 0.91 (0.77–1.08)
 rs10792258j T 0.20 . . . . . . . . . . . . 0.37 .010 0.79 (0.66–0.95)
ABCA7
 rs3752246 G 0.19 Naj et al,22 2011 0.19 5.8 × 10−7 1.15 (1.09–1.21) 0.04 .375 0.82 (0.53–1.27)
 rs3764650 G 0.11 Hollingworth et al,23 2011 . . . 4.5 × 10−17 1.23 (1.18–1.30) 0.28 .019 1.27 (1.04–1.55)
 rs3764647k G 0.04 . . . . . . . . . . . . 0.25 .0087 1.32 (1.07–1.63)
CD33
 rs3865444 A 0.32 Naj et al,22 2011 0.30 1.6 × 10−9 0.91 (0.88–0.93) 0.09 .732 0.95 (0.70–1.29)
 rs10419982l A 0.45 . . . . . . . . . . . . 0.40 .00054 1.38 (1.15–1.65)

Abbreviations: ABCA7, ATP-binding cassette, subfamily A (ABC1), member 7; AF, effect allele frequency; BIN1, bridging integrator 1; CD2AP, CD2-associated protein; CD33, myeloid-associated antigen CD33; CEU, HapMap’s CEPH (Utah residents with ancestry from Northern and Western Europe) Population; CLU, clusterin; CR1, complement component (3b/4b) receptor 1; ellipses, missing information; EPHA1, ephrin type-A receptor 1; GWAS, genome-wide association study; kb, kilobase; MS4A, the membrane-spanning 4A gene cluster; NPR, not previously reported as associated with Alzheimer disease in whites; NR, not reported; OR, odds ratio; PICALM, phosphatidylinositol binding clathrin assembly protein; SNP, single-nucleotide polymorphism.

a

Effect estimate directions differ between whites and African Americans.

b

This SNP was not previously reported as associated with Alzheimer disease in whites (NPR). The lowest P value is in CLU.

c

This SNP was NPR and is located 15 kb from rs3851179.

d

This SNP was NPR. This represents the lowest P value observed in PICALM.

e

This SNP was NPR and flanks rs744375, 6.5 kb away from rs744373.

f

This SNP was NPR. This represents the most significant P value observed in BIN1.

g

This SNP was NPR. This represents the lowest P value observed in the BIN1 region.

h

This SNP was NPR and flanks rs11767557.

i

This SNP was NPR. This represents the smallest P value observed in the region of EPHA1.

j

This SNP was NPR. This represents the smallest P value observed in the MS4A region.

k

This SNP was NPR. This represents the smallest P value observed in ABCA7.

l

This SNP was NPR and is 63 kb from rs3865444. This represents the lowest P value observed in the CD33 region.