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. 2020 May 13;16(7):983–1002. doi: 10.1002/alz.12099

TABLE 1.

IGAP loci associations stratified by H2 non‐carriers and H2 carriers

Unstratified f H2 non‐carriers f H2 carriers f
SNP a CHR c Position c Closest gene d Major/Minor c MAF e Nj g ORJ (95% CI) g P J g NM h ORm h PM h Nj g ORJ (95% CI) g PJ g NM h ORm h PM h Nj g ORJ (95% CI) g PJ g NM h ORm h PM h Epistatis P i
rs6656401 1 207692049 CR1 G/A 0.183 17833 1.15 (1.08‐1.21) 2.37E‐06 21 1.15 1.37E‐06 10854 1.13 (1.05‐1.21) 9.82E‐04 21 1.14 7.48E‐04 6979 1.17 (1.07‐1.28) 7.45E‐04 21 1.17 1.36E‐03 5.37E‐01
rs6733839 2 127892810 BIN1;CYP27C1 C/T 0.394 14091 1.23 (1.17‐1.3) 4.39E‐16 21 1.23 1.89E‐10 8627 1.23 (1.15‐1.31) 2.64E‐10 21 1.23 1.25E‐09 5464 1.24 (1.14‐1.35) 3.43E‐07 21 1.27 6.23E‐08 8.38E‐01
rs35349669 2 234068476 INPP5D C/T 0.482 17273 1.04(1‐1.09) 7.35E‐02 21 1.04 7.39E‐02 10535 1.04 (0.99‐1.11) 1.37E‐01 21 1.05 9.74E‐02 6738 1.03 (0.96‐1.11) 3.69E‐01 21 1.02 5.38E‐01 8.82E‐01
rs190982 5 88223420 MEF2C‐AS1 A/G 0.384 16317 0.94 (0.9‐0.98) 9.25E‐03 21 0.93 5.87E‐03 9911 0.93 (0.88‐0.99) 2.53E‐02 21 0.92 1.03E‐02 6406 0.95 (0.88‐1.02) 1.78E‐01 21 0.96 2.87E‐01 7.69E‐01
rs9271192 6 32578530 HLA‐DRB1;HLA‐DQA1 A/C 0.272 18208 1.1 (1.05‐1.15) 1.51E‐04 21 1.10 2.37E‐03 11080 1.14 (1.07‐1.21) 7.56E‐05 21 1.14 1.85E‐03 7128 1.04 (0.96‐1.13) 2.92E‐01 21 1.05 2.73E‐01 1.02E‐01
rs10948363 6 47487762 CD2AP A/G 0.274 18827 1.09 (1.04‐1.14) 5.18E‐04 21 1.09 5.22E‐04 11476 1.05 (0.98‐1.11) 1.56E‐01 21 1.05 1.47E‐01 7351 1.16 (1.07‐1.25) 1.60E‐04 21 1.16 6.81E‐04 3.47E‐02
rs2718058 7 37841534 GPR141;NME8 A/G 0.364 18336 0.93 (0.89‐0.98) 2.81E‐03 21 0.94 7.69E‐02 11182 0.94 (0.89‐1) 4.77E‐02 21 0.97 3.96E‐01 7154 0.92 (0.86‐0.99) 2.78E‐02 21 0.92 2.50E‐02 6.38E‐01
rs1476679 7 100004446 ZCWPW1/PILRB T/C 0.280 18617 0.92 (0.88‐0.97) 1.22E‐03 21 0.92 1.73E‐03 11346 0.88 (0.83‐0.94) 7.06E‐05 21 0.88 8.06E‐05 7271 0.99 (0.92‐1.07) 7.82E‐01 21 0.98 7.21E‐01 2.20E‐02
rs11771145 7 143110762 EPHA1‐AS1 G/A 0.334 17291 0.93 (0.89‐0.97) 1.97E‐03 21 0.93 4.22E‐03 10525 0.93 (0.88‐0.99) 1.85E‐02 21 0.93 2.87E‐02 6766 0.93 (0.86‐1) 4.27E‐02 21 0.93 6.38E‐02 8.76E‐01
rs28834970 8 27195121 PTK2B T/C 0.363 18538 1.13 (1.08‐1.18) 1.68E‐07 21 1.13 1.64E‐07 11305 1.14 (1.07‐1.2) 1.48E‐05 21 1.14 1.67E‐04 7233 1.12 (1.04‐1.2) 3.15E‐03 21 1.12 3.42E‐03 6.97E‐01
rs9331896 b 8 27467686 CLU T/C 0.377 16160 0.90 (0.86‐0.95) 2.45E‐05 NA NA NA 9842 0.91 (0.85‐0.96) 1.36E‐03 NA NA NA 6318 0.90 (0.84‐0.98) 9.41E‐03 NA NA NA 9.87E‐01
rs10838725 11 47557871 CELF1 T/C 0.316 18596 1.04 (0.99‐1.09) 1.25E‐01 21 1.04 9.93E‐02 11334 1.04 (0.98‐1.11) 1.63E‐01 21 1.04 2.03E‐01 7262 1.03 (0.96‐1.11) 4.20E‐01 21 1.04 2.99E‐01 7.52E‐01
rs983392 11 59923508 MS4A2;MS4A6A A/G 0.398 18095 0.87 (0.84‐0.91) 2.44E‐09 21 0.87 5.14E‐09 11017 0.87 (0.83‐0.93) 3.61E‐06 21 0.87 3.55E‐06 7078 0.87 (0.81‐0.93) 1.11E‐04 21 0.86 4.95E‐03 9.28E‐01
rs10792832 11 85867875 PICALM;EED G/A 0.355 18651 0.88 (0.84‐0.92) 7.90E‐09 21 0.88 9.90E‐09 11368 0.89 (0.84‐0.94) 3.32E‐05 21 0.89 7.71E‐05 7283 0.86 (0.8‐0.93) 5.00E‐05 21 0.85 4.90E‐05 5.56E‐01
rs11218343 11 121435587 SORL1 T/C 0.039 18816 0.76 (0.68‐0.84) 7.44E‐07 21 0.75 9.94E‐07 11465 0.8 (0.69‐0.92) 1.46E‐03 21 0.80 2.20E‐03 7351 0.69 (0.58‐0.83) 5.43E‐05 18 0.69 1.34E‐04 2.26E‐01
rs17125944 14 53400629 FERMT2 T/C 0.093 18809 1.12 (1.04‐1.21) 2.75E‐03 21 1.13 2.59E‐02 11459 1.11 (1.01‐1.22) 3.68E‐02 21 1.09 1.84E‐01 7350 1.15 (1.02‐1.29) 2.38E‐02 21 1.15 2.32E‐02 5.89E‐01
rs10498633 14 92926952 SLC24A4 G/T 0.217 18720 0.92 (0.88‐0.97) 2.27E‐03 21 0.93 5.80E‐03 11409 0.9 (0.84‐0.96) 1.45E‐03 21 0.90 2.50E‐03 7311 0.96 (0.88‐1.04) 3.27E‐01 21 0.97 5.18E‐01 2.21E‐01
rs8093731 18 29088958 DSG2 C/T 0.010 18683 0.94 (0.76‐1.16) 5.49E‐01 20 1.01 9.39E‐01 11389 0.9 (0.69‐1.18) 4.62E‐01 18 0.84 2.92E‐01 7294 0.99 (0.72‐1.38) 9.70E‐01 15 1.14 6.31E‐01 6.37E‐01
rs4147929 b 19 1063443 ABCA7 G/A 0.171 16429 1.14 (1.07‐1.21) 4.60E‐05 NA NA NA 10002 1.09 (1.01‐1.18) 2.97E‐02 NA NA NA 6427 1.21 (1.09‐1.33) 1.61E‐04 NA NA NA 1.34E‐01
rs3865444 19 51727962 CD33 C/A 0.303 18707 0.91 (0.87‐0.96) 1.78E‐04 21 0.91 1.70E‐04 11395 0.92 (0.87‐0.98) 8.80E‐03 21 0.92 1.14E‐02 7312 0.9 (0.84‐0.97) 6.84E‐03 21 0.89 3.35E‐03 6.27E‐01
rs7274581 20 55018260 CASS4 T/C 0.084 18599 0.87 (0.8‐0.94) 3.21E‐04 21 0.86 2.92E‐04 11333 0.88 (0.8‐0.98) 1.71E‐02 21 0.88 2.01E‐02 7266 0.84 (0.74‐0.95) 5.15E‐03 21 0.84 5.66E‐03 4.88E‐01
a

IGAP variants determined in the publication Lambert et al.21

b

SNPs rs4147929 and rs9331896 were filtered out of the original analysis due to the QC procedures in Boehme et al.27 They were evaluated separately for the joint analysis.

c

Chromosome, position, alleles from the February 2009 (GRCh37/hg19) build.

d

Nearest gene(s) located within ±100 kb of the IGAP SNP.

e

MAF calculated in PLINK derived from the unstratified genotypes.

f

Unstratified contains all subjects from the 21 ADGC cohorts used for analysis. The H2 tagging variant rs8070723 was used to stratify study participants into H2 non‐carriers (H1H1) and H2 carriers (H1H2+H2H2).

g

Joint analysis performed with logistic regression in PLINK using as covariates age, sex, cohort, and PC1‐3. Rs4147929 is missing in the GSK cohort. N, number of subjects analyzed; OR, odds ratio for AD risk for the minor allele; 95% CI, 95% confidence interval, P‐value.

h

Meta‐analysis performed with logistic regression analysis in PLINK using the random effects model, and using the covariates age, sex, and PC1‐3. Meta‐analysis could not be performed for rs4147929 and rs9331896. N, number of cohorts analyzed; OR, odds ratio, P‐value.

i

Epistasis analyses performed in R. All cohorts were combined and stratified into two groups by the H2 tagging variant rs8070723: H2 non‐carriers (H1H1) and H2 carriers (H1H2+H2H2). Results from the carrier model are shown.