Table 6-.
Summary of the analysis of protective/disease-modifying variants in Alzheimer’s disease cases and controls in the ADSP
| Protective_model <- glm(PHENO ~ Protective/disease-modifying variant + SEX + AGE + PC1 + PC2 + PC3 + PC4 + PC5, data = data, family = binomial) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| 19q13.31 : rs10423769, chr19:43100929:G>A | |||||||||||
| Ancestry | EUR | AFR | AMR | EAS | SAS | MDE | AJ | FIN | AAC | CAS | CAH |
| A1 | A | A | A | A | A | A | A | A | A | A | A |
| P | 0.460811 | 0.6021 | 0.215674 | NA | NA | 0.789232 | 0.46266 | NA | 0.842912 | NA | 0.201781 |
| OR (L95_U95) | 0.79711 (0.436315_1.45625) | 0.949949 (0.783198_1.1522) | 1.26959 (0.870087_1.85251) | NA | NA | 1.89966 (0.0171931_209.893) | 0.807628 (0.456669_1.4283) | NA | 1.01806 (0.852894_1.21521) | NA | 0.848645 (0.659614_1.09185) |
| APOE:rs449647, Chr19:44905307: A>T | |||||||||||
| Ancestry | EUR | AFR | AMR | EAS | SAS | MDE | AJ | FIN | AAC | CAS | CAH |
| A1 | T | T | T | T | T | T | T | T | T | T | T |
| P | 2.19e-14 | 6.62e-06 | 0.921403 | 0.410879 | 0.71756 | 0.126724 | 0.000246962 | 0.657878 | 0.0596323 | 0.935904 | 0.490397 |
| OR (L95_U95) | 0.723607 (0.66597_0.786231) | 1.37695 (1.19808_1.58252) | 1.00596 (0.894033_1.13189) | 2.47276 (0.285812_21.3935) | 0.940468 (0.67439_1.31153) | 0.25441 (0.0439125_1.47394) | 0.671781 (0.543053_0.831022) | 0.43746 (0.0112664_16.986) | 1.12355 (0.995282_1.26834) | 1.03813 (0.417042_2.58418) | 1.04671 (0.91935_1.19172) |
| TOMM40 :rs11556505, Chr19:44892887: C>T | |||||||||||
| Ancestry | EUR | AFR | AMR | EAS | SAS | MDE | AJ | FIN | AAC | CAS | CAH |
| A1 | T | T | T | T | T | T | T | T | T | T | T |
| P | 4.86e-108 | 0.280115 | 5.78e-15 | 0.999971 | 0.290208 | 0.390511 | 0.00013708 | 0.726914 | 0.00011157 | 0.504467 | 2.85e-07 |
| OR (L95_U95) | 2.29043 (2.12799_2.46527) | 1.12056 (0.911434_1.37768) | 1.76617 (1.53118_2.03722) | 0.999981 (0.36233_2.75981) | 1.18727 (0.863778_1.63191) | 3.89111 (0.175077_86.4808) | 1.61043 (1.26061_2.05732) | 1.62127 (0.107672_24.4124) | 1.38513 (1.17414_1.63403) | 1.41907 (0.50777_3.96587) | 1.56334 (1.31814_1.85415) |
| NOCT:rs13116075 , Chr4:139008878: A>G | |||||||||||
| Ancestry | EUR | AFR | AMR | EAS | SAS | MDE | AJ | FIN | AAC | CAS | CAH |
| A1 | G | G | G | G | G | G | G | G | G | G | G |
| P | 0.0874581 | 0.658188 | 0.113149 | 0.66702 | 0.9558 | 0.661009 | 0.142146 | 0.231494 | 0.180217 | 0.107993 | 0.705767 |
| OR (L95_U95) | 1.07114 (0.989957_1.15899) | 1.10373 (0.712821_1.709) | 0.865449 (0.723765_1.03487) | 0.343613 (0.00264628_44.6173) | 0.988192 (0.649261_1.50405) | 1.89182 (0.109489_32.688) | 0.831151 (0.649279_1.06397) | 188.49 (0.0353377_1005400.0) | 0.853469 (0.676933_1.07604) | 0.10942 (0.00736793_1.62499) | 0.965653 (0.80542_1.15776) |
| CASS4 :rs6024870 , Chr20:56422512: G>A | |||||||||||
| Ancestry | EUR | AFR | AMR | EAS | SAS | MDE | AJ | FIN | AAC | CAS | CAH |
| A1 | A | A | A | A | A | A | A | A | A | A | A |
| P | 0.317519 | 0.19334 | 0.947158 | NA | 0.743636 | 0.399733 | 0.159203 | NA | 0.604016 | 0.512028 | 0.79705 |
| OR (L95_U95) | 0.948467 (0.855001_1.05215) | 0.851492 (0.668311_1.08488) | 0.993588 (0.82148_1.20176) | NA | 1.17134 (0.454001_3.02213) | 3.55752 (0.185509_68.2227) | 0.836323 (0.652077_1.07263) | NA | 1.05138 (0.870015_1.27055) | 0.458625 (0.0446159_4.7144) | 1.02512 (0.848483_1.23854) |
| LRRC37A : rs2732703 , Chr17:46275856: T>G | |||||||||||
| Ancestry | EUR | AFR | AMR | EAS | SAS | MDE | AJ | FIN | AAC | CAS | CAH |
| A1 | G | G | G | G | G | G | G | G | G | G | G |
| P | 0.0147474 | 0.545618 | 0.580112 | NA | 0.80132 | 0.877837 | 0.0979924 | 0.78562 | 0.931261 | 0.717238 | 0.639068 |
| OR (L95_U95) | 0.900167 (0.8272_0.979571) | 0.862876 (0.534833_1.39212) | 0.95293 (0.803301_1.13043) | NA | 0.928456 (0.52079_1.65524) | 0.827929 (0.0745303_9.19716) | 0.803044 (0.619302_1.0413) | 1.46559 (0.0932775_23.0276) | 0.989343 (0.775568_1.26204) | 0.737015 (0.141339_3.84319) | 0.956805 (0.795579_1.1507) |
| Conditional_model <- glm(PHENO ~ Protective/disease-modifying variant + APOE_STATUS (ε4 carriers) +SEX + AGE + PC1 + PC2 + PC3 + PC4 + PC5, data = data, family = binomial) | |||||||||||
| 19q13.31 : rs10423769, chr19:43100929:G>A | |||||||||||
| Ancestry | EUR | AFR | AMR | EAS | SAS | MDE | AJ | FIN | AAC | CAS | CAH |
| A1 | A | A | A | A | A | A | A | A | A | A | A |
| P | 0.690443 | 0.517056 | 0.161042 | NA | NA | 0.70344 | 0.535244 | NA | 0.922067 | NA | 0.157721 |
| OR (L95_U95) | 0.879192 (0.466549_1.6568) | 0.936955 (0.769422_1.14097) | 1.31287 (0.897222_1.92108) | NA | NA | 2.51389 (0.0218339_289.443) | 0.832044 (0.465285_1.4879) | NA | 1.00909 (0.841704_1.20978) | NA | 0.831481 (0.643669_1.07409) |
| APOE :rs449647, Chr19:44905307: A>T | |||||||||||
| Ancestry | EUR | AFR | AMR | EAS | SAS | MDE | AJ | FIN | AAC | CAS | CAH |
| A1 | T | T | T | T | T | T | T | T | T | T | T |
| P | 0.438088 | 0.0624138 | 0.472261 | 0.43965 | 0.865612 | 0.139162 | 0.0285317 | 0.864837 | 0.496478 | 0.851361 | 0.941387 |
| OR (L95_U95) | 0.965782 (0.884422_1.05463) | 1.15042 (0.99276_1.33312) | 1.04487 (0.927005_1.17773) | 2.38768 (0.262626_21.7078) | 0.971482 (0.694882_1.35818) | 0.291295 (0.0568107_1.49361) | 0.780509 (0.625253_0.974316) | 1.6768 (0.00436235_644.531) | 0.956649 (0.841935_1.08699) | 1.09711 (0.416133_2.89248) | 0.995056 (0.871901_1.13561) |
| TOMM40 :rs11556505, Chr19:44892887: C>T | |||||||||||
| Ancestry | EUR | AFR | AMR | EAS | SAS | MDE | AJ | FIN | AAC | CAS | CAH |
| A1 | T | T | T | T | T | T | T | T | T | T | T |
| P | 3.05e-06 | 0.349246 | 0.258 | 0.305313 | 0.925043 | 0.306123 | 0.825232 | 0.864985 | 0.0409785 | 0.517952 | 0.0463152 |
| OR (L95_U95) | 1.24509 (1.1356_1.36513) | 1.10709 (0.894683_1.36993) | 1.12255 (0.918784_1.3715) | 0.386149 (0.0626103_2.38157) | 0.980508 (0.650674_1.47754) | 12.6053 (0.0983582_1615.46) | 1.03582 (0.757949_1.41555) | 1.35469 (0.0409377_44.8285) | 1.19548 (1.00735_1.41876) | 0.637351 (0.162678_2.49707) | 1.20744 (1.00308_1.45342) |
| NOCT :rs13116075 , Chr4:139008878: A>G | |||||||||||
| Ancestry | EUR | AFR | AMR | EAS | SAS | MDE | AJ | FIN | AAC | CAS | CAH |
| A1 | G | G | G | G | G | G | G | G | G | G | G |
| P | 0.11744 | 0.645244 | 0.119401 | 0.551474 | 0.995776 | 0.682833 | 0.228236 | 0.415815 | 0.190788 | 0.123526 | 0.623371 |
| OR (L95_U95) | 1.06849 (0.983453_1.16087) | 1.11107 (0.709591_1.7397) | 0.866307 (0.723148_1.03781) | 0.222352 (0.00157819_31.3274) | 1.00114 (0.657627_1.52408) | 0.664864 (0.0938476_4.71024) | 0.856635 (0.666008_1.10183) | 3.39754 (0.178546_64.6512) | 0.853379 (0.672949_1.08219) | 0.12043 (0.00814495_1.78066) | 0.954866 (0.794128_1.14814) |
| CASS4 :rs6024870 , Chr20:56422512: G>A | |||||||||||
| Ancestry | EUR | AFR | AMR | EAS | SAS | MDE | AJ | FIN | AAC | CAS | CAH |
| A1 | A | A | A | A | A | A | A | A | A | A | A |
| P | 0.166437 | 0.266129 | 0.885204 | NA | 0.722628 | 0.396827 | 0.0769097 | NA | 0.725645 | 0.491759 | 0.891828 |
| OR (L95_U95) | 0.925783 (0.829988_1.03263) | 0.868781 (0.678012_1.11322) | 1.01427 (0.836751_1.22946) | NA | 1.18792 (0.459014_3.07431) | 4.06585 (0.158516_104.287) | 0.795013 (0.616578_1.02509) | NA | 1.0353 (0.852927_1.25668) | 0.434108 (0.0402219_4.68526) | 1.0134 (0.836458_1.22778) |
| LRRC37A: rs2732703 , Chr17:46275856: T>G | |||||||||||
| Ancestry | EUR | AFR | AMR | EAS | SAS | MDE | AJ | FIN | AAC | CAS | CAH |
| A1 | G | G | G | G | G | G | G | G | G | G | G |
| P | 0.0206232 | 0.478694 | 0.481538 | NA | 0.761611 | 0.861743 | 0.181446 | 0.831894 | 0.872138 | 0.833465 | 0.648529 |
| OR (L95_U95) | 0.900245 (0.823603_0.98402) | 0.837245 (0.512161_1.36867) | 0.939807 (0.790605_1.11717) | NA | 0.91409 (0.511621_1.63316) | 0.806351 (0.0715386_9.08883) | 0.834828 (0.640625_1.0879) | 1.38359 (0.0690329_27.7305) | 0.979684 (0.763012_1.25788) | 0.838877 (0.163097_4.31471) | 0.957399 (0.793949_1.1545) |
| Conditional_model <- glm(PHENO ~ Protective/disease-modifying variant + APOE_STATUS (ε4/ε4) +SEX + AGE + PC1 + PC2 + PC3 + PC4 + PC5, data = data, family = binomial) | |||||||||||
| 19q13.31 : rs10423769, chr19:43100929:G>A | |||||||||||
| Ancestry | EUR | AFR | AMR | EAS | SAS | MDE | AJ | FIN | AAC | CAS | CAH |
| A1 | A | A | A | A | A | A | A | A | A | A | A |
| P | 0.520432 | 0.487737 | 0.242755 | NA | NA | 0.723333 | 0.464294 | NA | 0.7821 | NA | 0.116951 |
| OR (L95 U95) | 0.818862 (0.445176_1.50622) | 0.93305 (0.767187_1.13477) | 1.25453 (0.857515_1.83537) | NA | NA | 2.34504 (0.0209322_262.714) | 0.806588 (0.453563_1.43439) | NA | 1.02572 (0.8568_1.22794) | NA | 0.814618 (0.630416_1.05264) |
| APOE :rs449647, Chr19:44905307: A>T | |||||||||||
| Ancestry | EUR | AFR | AMR | EAS | SAS | MDE | AJ | FIN | AAC | CAS | CAH |
| A1 | T | T | T | T | T | T | T | T | T | T | T |
| P | 5.13e-07 | 0.00116208 | 0.65243 | 0.406828 | 0.713205 | 0.204203 | 0.00311608 | 0.937989 | 0.506202 | 0.940189 | 0.843606 |
| OR (L95_U95) | 0.80682 (0.741977_0.87733) | 1.26706 (1.09841_1.4616) | 1.02765 (0.912626_1.15718) | 2.44129 (0.296298_20.1146) | 0.939528 (0.673676_1.31029) | 0.362537 (0.0757061_1.73609) | 0.723028 (0.583137_0.896479) | 1.17291 (0.021098_65.2066) | 1.04321 (0.920878_1.1818) | 1.03564 (0.414924_2.58492) | 1.01332 (0.888485_1.1557) |
| TOMM40 :rs11556505, Chr19:44892887: C>T | |||||||||||
| Ancestry | EUR | AFR | AMR | EAS | SAS | MDE | AJ | FIN | AAC | CAS | CAH |
| A1 | T | T | T | T | T | T | T | T | T | T | T |
| P | 1.68e-58 | 0.375778 | 1.22e-07 | 0.649911 | 0.24013 | 0.847088 | 0.00962134 | 0.823812 | 0.00964987 | 0.494246 | 0.000521882 |
| OR (L95_U95) | 1.95842 (1.80479_2.12513) | 1.09968 (0.891141_1.35703) | 1.5297 (1.30682_1.79058) | 1.38741 (0.337396_5.70517) | 1.21776 (0.876594_1.69171) | 1.26953 (0.112259_14.357) | 1.41037 (1.08715_1.82968) | 1.25464 (0.17031_9.24275) | 1.25348 (1.05637_1.48738) | 1.46486 (0.490248_4.37702) | 1.37305 (1.14789_1.64237) |
| NOCT:rs13116075 , Chr4:139008878: A>G | |||||||||||
| Ancestry | EUR | AFR | AMR | EAS | SAS | MDE | AJ | FIN | AAC | CAS | CAH |
| A1 | G | G | G | G | G | G | G | G | G | G | G |
| P | 0.0886405 | 0.577482 | 0.126453 | 0.748873 | 0.954283 | 0.742716 | 0.138021 | 0.529144 | 0.183083 | 0.104656 | 0.648668 |
| OR (L95_U95) | 1.07213 (0.989528_1.16163) | 1.13356 (0.729266_1.762) | 0.869347 (0.726455_1.04035) | 0.424654 (0.00224227_80.4235) | 0.987788 (0.648967_1.5035) | 0.713686 (0.0952421_5.34792) | 0.828076 (0.645363_1.06252) | 2.58464 (0.134278_49.7502) | 0.851783 (0.672605_1.07869) | 0.105682 (0.00700063_1.59537) | 0.958323 (0.797957_1.15092) |
| CASS4 :rs6024870 , Chr20:56422512: G>A | |||||||||||
| Ancestry | EUR | AFR | AMR | EAS | SAS | MDE | AJ | FIN | AAC | CAS | CAH |
| A1 | A | A | A | A | A | A | A | A | A | A | A |
| P | 0.315877 | 0.203848 | 0.932446 | NA | 0.74473 | 0.985781 | 0.152267 | NA | 0.500034 | 0.509982 | 0.826824 |
| OR (L95_U95) | 0.947416 (0.852505_1.05289) | 0.852854 (0.667192_1.09018) | 0.991742 (0.818715_1.20134) | NA | 1.17055 (0.45363_3.02051) | 0.979617 (0.101731_9.43317) | 0.8319 (0.646608_1.07029) | NA | 1.06851 (0.881347_1.29542) | 0.456796 (0.04441_4.69855) | 1.02149 (0.844336_1.23581) |
| LRRC37A: rs2732703 , Chr17:46275856: T>G | |||||||||||
| Ancestry | EUR | AFR | AMR | EAS | SAS | MDE | AJ | FIN | AAC | CAS | CAH |
| A1 | G | G | G | G | G | G | G | G | G | G | G |
| P | 0.0170534 | 0.526575 | 0.657118 | NA | 0.800316 | 0.80885 | 0.108589 | 0.842417 | 0.84495 | 0.720352 | 0.691408 |
| OR (L95_U95) | 0.90071 (0.826556_0.981517) | 0.854763 (0.525895_1.38929) | 0.961802 (0.809848_1.14227) | NA | 0.928096 (0.52057_1.65465) | 0.767101 (0.0895205_6.57328) | 0.806879 (0.620834_1.04868) | 1.38422 (0.0561144_34.1458) | 0.975534 (0.761079_1.25042) | 0.739306 (0.141463_3.86371) | 0.963032 (0.799585_1.15989) |
| r2_model <- lm(Protective/disease-modifying variant ~ APOESTATUS (ε4 carriers) +SEX + AGE + PC1 + PC2 + PC3 + PC4 + PC5, data = data) | |||||||||||
| 19q13.31: rs10423769, chr19:43100929:G>A | |||||||||||
| Ancestry | EUR | AFR | AMR | EAS | SAS | MDE | AJ | FIN | AAC | CAS | CAH |
| Multiple R-squared | 0.005848 | 0.006813 | 0.01403 | NA | NA | 0.06651 | 0.003517 | NA | 0.008922 | NA | 0.01368 |
| Adjusted R-squared | 0.00507 | 0.003417 | 0.01247 | NA | NA | −0.2101 | −0.00456 | NA | 0.005956 | NA | 0.01079 |
| F-statistic | 7.511 | 2.006 | 8.972 | NA | NA | 0.2404 | 0.4354 | NA | 3.008 | NA | 4.728 |
| p-value (F-statistic) | 4.81e-10 | 0.04213 | 2.69e-12 | NA | NA | 0.9792 | 0.9002 | NA | 0.002308 | NA | 8.90e-06 |
| APOE :rs449647, Chr19:44905307: A>T | |||||||||||
| Ancestry | EUR | AFR | AMR | EAS | SAS | MDE | AJ | FIN | AAC | CAS | CAH |
| Multiple R-squared | 0.05969 | 0.09666 | 0.008391 | 0.1156 | 0.02943 | 0.1789 | 0.07881 | 0.6671 | 0.0556 | 0.07086 | 0.01471 |
| Adjusted R-squared | 5.90e-02 | 0.09357 | 0.006819 | 0.01455 | 0.02626 | −0.06436 | 0.07134 | 0.4769 | 0.05278 | 0.01851 | 0.01182 |
| F-statistic | 81.04 | 31.3 | 5.336 | 1.144 | 9.272 | 0.7354 | 10.55 | 3.507 | 19.67 | 1.354 | 5.091 |
| p-value (F-statistic) | < 2.2e-16 | < 2.2e-16 | 1.08e-06 | 0.3455 | 1.15e-12 | 0.6598 | 2.72e-14 | 0.01951 | < 2.2e-16 | 0.2221 | 2.62e-06 |
| TOMM40 :rs11556505, Chr19:44892887: C>T | |||||||||||
| Ancestry | EUR | AFR | AMR | EAS | SAS | MDE | AJ | FIN | AAC | CAS | CAH |
| Multiple R-squared | 0.4047 | 0.005166 | 0.5032 | 0.5528 | 0.3681 | 0.4932 | 0.4053 | 0.2905 | 0.03025 | 0.4191 | 0.1588 |
| Adjusted R-squared | 4.04e-01 | 0.001765 | 5.02e-01 | 0.5017 | 0.366 | 0.3431 | 0.4005 | −0.1149 | 0.02735 | 0.3863 | 0.1563 |
| F-statistic | 867.9 | 1.519 | 638.5 | 10.82 | 178.1 | 3.285 | 84.07 | 0.7166 | 10.42 | 12.8 | 64.34 |
| p-value (F-statistic) | < 2.2e-16 | 0.1453 | < 2.2e-16 | 8.93e-10 | < 2.2e-16 | 0.009537 | < 2.2e-16 | 0.6747 | 1.76e-14 | 9.05e-14 | < 2.2e-16 |
| AOCT:rs13116075 , Chr4:139008878: A>G | |||||||||||
| Ancestry | EUR | AFR | AMR | EAS | SAS | MDE | AJ | FIN | AAC | CAS | CAH |
| Multiple R-squared | 0.001905 | 0.00331 | 0.04212 | 0.1196 | 0.01192 | 0.2339 | 0.01113 | 0.4501 | 0.02384 | 0.1287 | 0.007236 |
| Adjusted R-squared | 0.001124 | −9.73E-05 | 0.0406 | 0.01903 | 0.008685 | 0.006878 | 0.003112 | 0.1359 | 0.02091 | 0.07962 | 0.004324 |
| F-statistic | 2.437 | 0.9714 | 27.72 | 1.189 | 3.688 | 1.03 | 1.388 | 1.432 | 8.159 | 2.622 | 2.485 |
| p-value (F-statistic) | 0.01247 | 0.4564 | < 2.2e-16 | 0.3181 | 0.0002741 | 0.4381 | 0.1974 | 0.2659 | 5.90e-11 | 0.01045 | 0.01101 |
| CASS4 :rs6024870 , Chr20:56422512: G>A | |||||||||||
| Ancestry | EUR | AFR | AMR | EAS | SAS | MDE | AJ | FIN | AAC | CAS | CAH |
| Multiple R-squared | 0.005311 | 0.008006 | 0.04053 | NA | 0.003495 | 0.2169 | 0.009504 | NA | 0.001664 | 0.09364 | 0.006718 |
| Adjusted R-squared | 0.004532 | 0.004614 | 0.03901 | NA | 0.0002362 | −0.01509 | 0.001476 | NA | −0.001323 | 0.04258 | 0.003805 |
| F-statistic | 6.818 | 2.361 | 26.63 | NA | 1.072 | 0.935 | 1.184 | NA | 0.5571 | 1.834 | 2.306 |
| p-value (F-statistic) | 5.75e-09 | 0.01578 | < 2.2e-16 | NA | 0.3794 | 0.5046 | 0.3055 | NA | 0.8136 | 0.07543 | 0.0184 |
| LRRC37A: rs2732703 , Chr17:46275856: T>G | |||||||||||
| Ancestry | EUR | AFR | AMR | EAS | SAS | MDE | AJ | FIN | AAC | CAS | CAH |
| Multiple R-squared | 0.007921 | 0.03169 | 0.07651 | NA | 0.01552 | 0.3253 | 0.01275 | 0.3684 | 0.03173 | 0.0346 | 0.008147 |
| Adjusted R-squared | 0.007144 | 0.02838 | 0.07505 | NA | 0.0123 | 0.1254 | 0.004751 | 0.007558 | 0.02883 | −0.01979 | 0.005237 |
| F-statistic | 10.19 | 9.574 | 52.24 | NA | 4.821 | 1.627 | 1.594 | 1.021 | 10.95 | 0.6361 | 2.8 |
| p-value (F-statistic) | 2.74e-14 | 3.99e-13 | < 2.2e-16 | NA | 6.59e-06 | 0.1635 | 0.1223 | 0.4641 | 2.65e-15 | 0.7463 | 0.004337 |
| r2_model <- lm(Protective/disease-modifying variant ~ APOESTATUS (ε4/ε4) +SEX + AGE + PC1 + PC2 + PC3 + PC4 + PC5, data = data) | |||||||||||
| 19q13.31: rs10423769, chr19:43100929:G>A | |||||||||||
| Ancestry | EUR | AFR | AMR | EAS | SAS | MDE | AJ | FIN | AAC | CAS | CAH |
| Multiple R-squared | 0.005736 | 0.007183 | 0.0141 | NA | NA | 0.05772 | 0.00307 | NA | 0.0089 | NA | 0.01519 |
| Adjusted R-squared | 0.004957 | 0.003789 | 0.01254 | NA | NA | −0.2215 | −0.00501 | NA | 0.005934 | NA | 0.0123 |
| F-statistic | 7.366 | 2.116 | 9.019 | NA | NA | 0.2067 | 0.38 | NA | 3.001 | NA | 5.258 |
| p-value (F-statistic) | 8.10e-10 | 0.03127 | 2.27e-12 | NA | NA | 0.9871 | 0.9315 | NA | 0.00236 | NA | 1.49e-06 |
| APOE :rs449647, Chr19:44905307: A>T | |||||||||||
| Ancestry | EUR | AFR | AMR | EAS | SAS | MDE | AJ | FIN | AAC | CAS | CAH |
| Multiple R-squared | 0.0319 | 0.04362 | 0.005569 | 0.1584 | 0.02047 | 0.1899 | 0.03783 | 0.445 | 0.02097 | 0.04018 | 0.01183 |
| Adjusted R-squared | 3.11e-02 | 0.04035 | 0.003992 | 0.0622 | 0.01727 | −0.05015 | 0.03003 | 0.1279 | 0.01804 | −0.01389 | 0.008934 |
| F-statistic | 42.07 | 13.34 | 3.531 | 1.647 | 6.391 | 0.7911 | 4.85 | 1.403 | 7.155 | 0.7431 | 4.082 |
| p-value (F-statistic) | < 2.2e-16 | < 2.2e-16 | 0.0004401 | 0.1274 | 3.05e-08 | 0.6149 | 6.99e-06 | 0.2767 | 2.06e-09 | 0.6533 | 7.59e-05 |
| TOMM40 :rs11556505, Chr19:44892887: C>T | |||||||||||
| Ancestry | EUR | AFR | AMR | EAS | SAS | MDE | AJ | FIN | AAC | CAS | CAH |
| Multiple R-squared | 0.2721 | 0.005496 | 0.1374 | 0.4969 | 0.07396 | 0.5143 | 0.1281 | 0.3759 | 0.02289 | 0.2014 | 0.08108 |
| Adjusted R-squared | 2.72e-01 | 0.002096 | 1.36e-01 | 0.4394 | 0.07093 | 0.3704 | 0.1211 | 0.01934 | 0.01996 | 0.1564 | 0.07838 |
| F-statistic | 477.2 | 1.617 | 100.4 | 8.642 | 24.42 | 3.573 | 18.13 | 1.054 | 7.826 | 4.476 | 30.08 |
| p-value (F-statistic) | < 2.2e-16 | 0.1149 | < 2.2e-16 | 4.07e-08 | < 2.2e-16 | 0.00599 | < 2.2e-16 | 0.4443 | 1.93e-10 | 7.29e-05 | < 2.2e-16 |
| NOCT:rs13116075 , Chr4:139008878: A>G | |||||||||||
| Ancestry | EUR | AFR | AMR | EAS | SAS | MDE | AJ | FIN | AAC | CAS | CAH |
| Multiple R-squared | 0.001848 | 0.003495 | 0.04217 | 0.1926 | 0.0117 | 0.2291 | 0.00869 | 0.4587 | 0.02382 | 0.1338 | 0.00723 |
| Adjusted R-squared | 0.001066 | 8.79E-05 | 0.04065 | 0.1004 | 0.008469 | 0.0007037 | 0.0006552 | 0.1493 | 0.02089 | 0.08501 | 0.004317 |
| F-statistic | 2.363 | 1.026 | 27.76 | 2.088 | 3.62 | 1.003 | 1.082 | 1.483 | 8.152 | 2.742 | 2.482 |
| p-value (F-statistic) | 0.01543 | 0.4139 | < 2.2e-16 | 0.04845 | 0.0003401 | 0.4565 | 0.3735 | 0.248 | 6.05e-11 | 0.007637 | 0.01109 |
| CASS4 :rs6024870 , Chr20:56422512: G>A | |||||||||||
| Ancestry | EUR | AFR | AMR | EAS | SAS | MDE | AJ | FIN | AAC | CAS | CAH |
| Multiple R-squared | 0.005269 | 0.007486 | 0.04021 | NA | 0.003431 | 0.1763 | 0.006623 | NA | 0.001632 | 0.09397 | 0.006616 |
| Adjusted R-squared | 0.00449 | 0.004093 | 0.03868 | NA | 0.0001714 | −0.06771 | −0.001429 | NA | −0.001357 | 0.04292 | 0.003701 |
| F-statistic | 6.763 | 2.206 | 26.41 | NA | 1.053 | 0.7226 | 0.8225 | NA | 0.546 | 1.841 | 2.27 |
| p-value (F-statistic) | 6.97e-09 | 0.02438 | < 2.2e-16 | NA | 0.3939 | 0.6703 | 0.5827 | NA | 0.8223 | 0.07417 | 0.02034 |
| LRRC37A: rs2732703, Chr17:46275856: T>G | |||||||||||
| Ancestry | EUR | AFR | AMR | EAS | SAS | MDE | AJ | FIN | AAC | CAS | CAH |
| Multiple R-squared | 0.007924 | 0.03166 | 0.0766 | NA | 0.01559 | 0.3186 | 0.009751 | 0.2984 | 0.03179 | 0.03813 | 0.008379 |
| Adjusted R-squared | 0.007147 | 0.02835 | 0.07514 | NA | 0.01237 | 0.1167 | 0.001725 | −0.1026 | 0.02889 | −0.01606 | 0.00547 |
| F-statistic | 10.2 | 9.563 | 52.3 | NA | 4.843 | 1.578 | 1.215 | 0.7442 | 10.97 | 0.7036 | 2.88 |
| p-value (F-statistic) | 2.70e-14 | 4.14e-13 | < 2.2e-16 | NA | 6.11e-06 | 0.1781 | 0.2866 | 0.6539 | 2.44e-15 | 0.688 | 0.0034 |
| Interactionmodel <- glm(PHENO ~ Protective/disease-modifying variant * APOESTATUS (ε4 carriers) +SEX + AGE + PC1 + PC2 + PC3 + PC4 + PC5, data = data, family = binomial) | |||||||||||
| 19q13.31: rs10423769, chr19:43100929:G>A | |||||||||||
| Ancestry | EUR | AFR | AMR | EAS | SAS | MDE | AJ | FIN | AAC | CAS | CAH |
| P | −0.318826 | −4.166e-01 | 4.690e-01 | NA | NA | NA | 0.4752150 | NA | −0.1165126 | NA | 1.433e-01 |
| Std. Error | 0.708762 | 1.989e-01 | 4.654e-01 | NA | NA | NA | 0.6321330 | NA | 0.1847811 | NA | 2.718e-01 |
| z value | −0.450 | −2.095 | 1.008 | NA | NA | NA | 0.752 | NA | −0.631 | NA | 0.527 |
| p-value | 0.652829 | 0.03619 | 0.313568 | NA | NA | NA | 0.4522 | NA | 0.52834 | NA | 0.598 |
| APOE :rs449647, Chr19:44905307: A>T | |||||||||||
| Ancestry | EUR | AFR | AMR | EAS | SAS | MDE | AJ | FIN | AAC | CAS | CAH |
| P | −0.270222 | −1.446e-02 | −2.146e-01 | −1.31410 | −0.41516 | −17.92462 | −0.3188204 | NA | −0.2674458 | −0.28649 | 9.553e-02 |
| Std. Error | 0.105633 | 1.494e-01 | 1.423e-01 | 2.47308 | 0.50059 | 2971.41668 | 0.2675842 | NA | 0.1298759 | 1.13455 | 1.405e-01 |
| z value | −2.558 | −0.097 | −1.508 | −0.531 | −0.829 | −0.006 | −1.191 | NA | −2.059 | −0.253 | 0.680 |
| p-value | 0.010524 | 0.92290 | 0.131445 | 0.595167 | 0.406911 | 0.9952 | 0.2335 | NA | 0.03947 | 0.800642 | 0.497 |
| TOMM40 :rs11556505, Chr19:44892887: C>T | |||||||||||
| Ancestry | EUR | AFR | AMR | EAS | SAS | MDE | AJ | FIN | AAC | CAS | CAH |
| P | 3.048e-01 | −1.037e-01 | 4.267e-01 | −1.84506 | −4.491e-02 | −10.51189 | 0.2308497 | 50.468 | 0.0356318 | −0.77961 | 1.709e-01 |
| Std. Error | 9.651e-02 | 2.173e-01 | 2.268e-01 | 1.98319 | 4.240e-01 | 2444.76386 | 0.3406798 | 3499.371 | 0.1757837 | 1.42636 | 1.915e-01 |
| z value | 3.158 | −0.477 | 1.882 | −0.930 | −0.106 | −0.004 | 0.678 | 0.014 | 0.203 | −0.547 | 0.892 |
| p-value | 0.001586 | 0.63323 | 0.059868 | 0.35219 | 0.915644 | 0.9966 | 0.49802 | 0.988 | 0.83937 | 0.584671 | 0.372 |
| AOCT:rs13116075 , Chr4:139008878: A>G | |||||||||||
| Ancestry | EUR | AFR | AMR | EAS | SAS | MDE | AJ | FIN | AAC | CAS | CAH |
| P | −8.385e-02 | −9.510e-01 | 7.260e-02 | NA | 0.26446 | −3.81041 | −0.2010145 | −5.534e+02 | 0.5046073 | −1.385e+00 | 2.081e-01 |
| Std. Error | 8.649e-02 | 4.567e-01 | 2.000e-01 | NA | 0.49224 | 2.97982 | 0.2679418 | 2.485e+06 | 0.2500546 | 3.982e+03 | 2.023e-01 |
| z value | −0.969 | −2.082 | 0.363 | NA | 0.537 | −1.279 | −0.750 | 0.000 | 2.018 | 0.000 | 1.029 |
| p-value | 0.33232 | 0.03732 | 0.716605 | NA | 0.591085 | 0.2010 | 0.4531 | 1.000 | 0.043592 | 0.99972 | 0.304 |
| CASS4 :rs6024870 , Chr20:56422512: G>A | |||||||||||
| Ancestry | EUR | AFR | AMR | EAS | SAS | MDE | AJ | FIN | AAC | CAS | CAH |
| P | −2.061e-01 | −9.165e-02 | 1.605e-01 | NA | −0.14240 | −17.90442 | −0.2340929 | NA | 0.1964231 | −1.592e+01 | −4.237e-01 |
| Std. Error | 1.121e-01 | 2.531e-01 | 2.191e-01 | NA | 1.25526 | 2623.75448 | 0.2607464 | NA | 0.2011266 | 1.264e+03 | 2.070e-01 |
| z value | −1.839 | −0.362 | 0.732 | NA | −0.113 | −0.007 | −0.898 | NA | 0.977 | −0.013 | −2.047 |
| p-value | 0.065858 | 0.71722 | 0.463960 | NA | 0.909678 | 0.9946 | 0.3693 | NA | 0.32876 | 0.989947 | 0.0406 |
| LRRC37A: rs2732703, Chr17:46275856: T>G | |||||||||||
| Ancestry | EUR | AFR | AMR | EAS | SAS | MDE | AJ | FIN | AAC | CAS | CAH |
| P | −6.999e-03 | 3.639e-01 | 3.705e-01 | NA | −0.14487 | −0.20542 | −0.3455109 | NA | −0.2151586 | −15.95199 | 8.660e-02 |
| Std. Error | 9.252e-02 | 5.076e-01 | 1.866e-01 | NA | 0.67397 | 2.71021 | 0.2772725 | NA | 0.2525163 | 1689.31304 | 2.043e-01 |
| z value | −0.076 | 0.717 | 1.985 | NA | −0.215 | −0.076 | −1.246 | NA | −0.852 | −0.009 | 0.424 |
| p-value | 0.939698 | 0.47344 | 0.047098 | NA | 0.829805 | 0.9396 | 0.2127 | NA | 0.39418 | 0.992466 | 0.672 |
| Interaction model <- glm(PHENO ~ Protective/disease-modifying variant * APOESTATUS (ε4/ε4) +SEX + AGE + PC1 + PC2 + PC3 + PC4 + PC5, data = data, family = binomial) | |||||||||||
| 19q13.31: rs10423769, chr19:43100929:G>A | |||||||||||
| Ancestry | EUR | AFR | AMR | EAS | SAS | MDE | AJ | FIN | AAC | CAS | CAH |
| P | 4.911e+00 | −1.297e-01 | 3.386e-01 | NA | NA | NA | 6.083e+00 | NA | −0.0109888 | NA | −1.266e-01 |
| Std. Error | 6.962e+01 | 1.673e-01 | 6.141e-01 | NA | NA | NA | 1.881e+02 | NA | 0.2050836 | NA | 2.496e-01 |
| z value | 0.071 | −0.775 | 0.551 | NA | NA | NA | 0.032 | NA | −0.054 | NA | −0.507 |
| p-value | 0.9438 | 0.43845 | 0.581417 | NA | NA | NA | 0.974203 | NA | 0.95727 | NA | 0.611873 |
| APOE :rs449647, Chr19:44905307: A>T | |||||||||||
| Ancestry | EUR | AFR | AMR | EAS | SAS | MDE | AJ | FIN | AAC | CAS | CAH |
| P | 1.985e-01 | 3.898e-02 | −6.337e-01 | 7.06937 | −6.024637 | NA | NA | NA | −0.4090145 | 7.737451 | −6.361e-02 |
| Std. Error | 3.794e-01 | 1.254e-01 | 2.572e-01 | 872.99690 | 187.324036 | NA | NA | NA | 0.1331053 | 688.428638 | 1.580e-01 |
| z value | 0.523 | 0.311 | −2.464 | 0.008 | −0.032 | NA | NA | NA | −3.073 | 0.011 | −0.403 |
| p-value | 0.6008 | 0.755964 | 0.013753 | 0.993539 | 0.974343 | NA | NA | NA | 0.00212 | 0.991033 | 0.687273 |
| TOMM40 :rs11556505, Chr19:44892887: C>T | |||||||||||
| Ancestry | EUR | AFR | AMR | EAS | SAS | MDE | AJ | FIN | AAC | CAS | CAH |
| P | −2.868e-01 | −1.377e-01 | −3.712e-02 | −7.69280 | 0.007408 | 5.14876 | −0.0208789 | −1.042e+02 | −0.1621401 | −7.062849 | −1.911e-01 |
| Std. Error | 8.295e-02 | 1.929e-01 | 1.600e-01 | 868.83988 | 0.678194 | 2797.44372 | 0.2745880 | 4.104e+05 | 0.1470801 | 727.699410 | 1.585e-01 |
| z value | −3.457 | −0.714 | −0.232 | −0.009 | 0.011 | 0.002 | −0.076 | 0.000 | −1.102 | −0.010 | −1.206 |
| p-value | 0.000546 | 0.475415 | 0.816578 | 0.992936 | 0.991284 | 0.9985 | 0.9394 | 1.000 | 0.27029 | 0.992256 | 0.227812 |
| NOCT:rs13116075 , Chr4:139008878: A>G | |||||||||||
| Ancestry | EUR | AFR | AMR | EAS | SAS | MDE | AJ | FIN | AAC | CAS | CAH |
| P | −1.127e-01 | −9.841e-01 | −6.797e-01 | NA | −5.758776 | NA | 0.1252292 | −1.879e+02 | 0.1242855 | NA | −4.846e-01 |
| Std. Error | 9.604e-02 | 5.861e-01 | 3.291e-01 | NA | 194.924414 | NA | 0.4583244 | 2.720e+05 | 0.2773288 | NA | 2.277e-01 |
| z value | −1.173 | −1.679 | −2.065 | NA | −0.030 | NA | 0.273 | −0.001 | 0.448 | NA | −2.128 |
| p-value | 0.2407 | 0.093119 | 0.038876 | NA | 0.976431 | NA | 0.78467 | 0.999 | 0.6540 | NA | 0.033307 |
| CASS4 :rs6024870 , Chr20:56422512: G>A | |||||||||||
| Ancestry | EUR | AFR | AMR | EAS | SAS | MDE | AJ | FIN | AAC | CAS | CAH |
| P | −6.057e-02 | 1.027e-01 | −2.230e-02 | NA | −5.08657 | −6.10931 | −0.3588910 | NA | 0.1269480 | −6.715306 | −1.595e-02 |
| Std. Error | 1.280e-01 | 2.424e-01 | 2.954e-01 | NA | 267.70598 | 2797.44428 | 0.3317201 | NA | 0.2388870 | 727.699378 | 2.476e-01 |
| z value | −0.473 | 0.424 | −0.075 | NA | −0.019 | −0.002 | −1.082 | NA | 0.531 | −0.009 | −0.064 |
| p-value | 0.6361 | 0.671842 | 0.939822 | NA | 0.984841 | 0.9983 | 0.27929 | NA | 0.59513 | 0.992637 | 0.949 |
| LRRC37A: rs2732703 , Chr17:46275856: T>G | |||||||||||
| Ancestry | EUR | AFR | AMR | EAS | SAS | MDE | AJ | FIN | AAC | CAS | CAH |
| P | 8.827e-02 | 1.163e-01 | 2.941e-02 | NA | −5.49623 | 5.63281 | −0.1043969 | −1.440e+02 | 0.1053866 | NA | −9.881e-02 |
| Std. Error | 1.098e-01 | 4.620e-01 | 2.958e-01 | NA | 218.06889 | 2797.44375 | 0.4237288 | 2.458e+05 | 0.2752225 | NA | 2.549e-01 |
| z value | 0.804 | 0.252 | 0.099 | NA | −0.025 | 0.002 | −0.246 | −0.001 | 0.383 | NA | −0.388 |
| p-value | 0.4215 | 0.801198 | 0.920809 | NA | 0.979892 | 0.9984 | 0.80539 | 1.000 | 0.70178 | NA | 0.698256 |
| Conditionalmodel <- glm(PHENO ~ Protective/disease-modifying variant + APOESTATUS (ε3/ε3) +SEX + AGE + PC1 + PC2 + PC3 + PC4 + PC5, data = data, family = binomial) | |||||||||||
| 19q13.31: rs10423769, chr19:43100929:G>A | |||||||||||
| Ancestry | EUR | AFR | AMR | EAS | SAS | MDE | AJ | FIN | AAC | CAS | CAH |
| A1 | A | A | A | A | A | A | A | A | A | A | A |
| P | 0.519217 | 0.508413 | 0.199474 | NA | NA | 0.720057 | 0.490052 | NA | 0.964739 | NA | 0.164826 |
| OR (L95_U95) | 0.8154 (0.438395_1.51662) | 0.936386 (0.770645_1.13777) | 1.28189 (0.877204_1.87326) | NA | NA | 2.4021 (0.0199145_289.744) | 0.816622 (0.459406_1.45159) | NA | 0.995971 (0.832748_1.19119) | NA | 0.835427 (0.648215_1.07671) |
| APOE :rs449647, Chr19:44905307: A>T | |||||||||||
| Ancestry | EUR | AFR | AMR | EAS | SAS | MDE | AJ | FIN | AAC | CAS | CAH |
| A1 | T | T | T | T | T | T | T | T | T | T | T |
| P | 3.76e-09 | 0.000378349 | 0.843162 | 0.409142 | 0.744106 | 0.139232 | 0.00257546 | 0.220398 | 0.536594 | 0.790636 | 0.861296 |
| OR (L95_U95) | 0.774637 (0.71158_0.843283) | 1.29317 (1.12226_1.49011) | 1.01206 (0.898723_1.13969) | 2.50033 (0.283747_22.0325) | 0.946117 (0.678434_1.31942) | 0.284837 (0.0539092_1.50498) | 0.716756 (0.577206_0.890043) | .0239989 (6.15937e-05_9.35072 | 1.03989 (0.918565_1.17724) | 0.880239 (0.34325_2.25731) | 1.01175 (0.887525_1.15335) |
| TOMM40 :rs11556505, Chr19:44892887: C>T | |||||||||||
| Ancestry | EUR | AFR | AMR | EAS | SAS | MDE | AJ | FIN | AAC | CAS | CAH |
| A1 | T | T | T | T | T | T | T | T | T | T | T |
| P | 1.28e-38 | 0.50568 | 0.000100648 | 0.931317 | 0.915364 | 0.49694 | 0.0510141 | 0.649767 | 0.00876273 | 0.688142 | 0.00210663 |
| OR (L95_U95) | 1.8019 (1.64879_1.96923) | 1.07366 (0.870902_1.32363) | 1.43907 (1.19788_1.72882) | 0.946922 (0.273961_3.27296) | 1.02006 (0.707227_1.47127) | 2.39398 (0.192874_29.7145) | 1.33147 (0.998739_1.77504) | 1.46764 (0.280186_7.68758) | 1.25301 (1.05855_1.4832) | 0.779007 (0.230106_2.63727) | 1.33379 (1.11007_1.60258) |
| AOCT:rs13116075 , Chr4:139008878: A>G | |||||||||||
| Ancestry | EUR | AFR | AMR | EAS | SAS | MDE | AJ | FIN | AAC | CAS | CAH |
| A1 | G | G | G | G | G | G | G | G | G | G | G |
| P | 0.0921729 | 0.579616 | 0.111308 | 0.658318 | 0.983852 | 0.690334 | 0.205043 | 0.492526 | 0.159087 | 0.150941 | 0.597635 |
| OR (L95_U95) | 1.07181 (0.988702_1.1619) | 1.13268 (0.728891_1.76017) | 0.863958 (0.721646_1.03434) | 0.332386 (0.00252112_43.822) | 0.99567 (0.654064_1.51569) | 1.79433 (0.101114_31.8415) | 0.850932 (0.66294_1.09223) | 3.02023 (0.128563_70.9521) | 0.844765 (0.667978_1.06834) | 0.139696 (0.00952012_2.04987) | 0.951919 (0.792742_1.14306) |
| CASS4 :rs6024870 , Chr20:56422512: G>A | |||||||||||
| Ancestry | EUR | AFR | AMR | EAS | SAS | MDE | AJ | FIN | AAC | CAS | CAH |
| A1 | A | A | A | A | A | A | A | A | A | A | A |
| P | 0.198142 | 0.2355 | 0.895017 | NA | 0.733941 | 0.317651 | 0.132828 | NA | 0.699167 | 0.495562 | 0.816941 |
| OR (L95_U95) | 0.93265 (0.838685_1.03714) | 0.862441 (0.675375_1.10132) | 1.01298 (0.83637_1.22689) | NA | 1.17936 (0.455509_3.05349) | 5.57921 (0.191552_162.501) | 0.824916 (0.641812_1.06026) | NA | 1.0385 (0.857433_1.2578) | 0.442584 (0.0424502_4.61436) | 1.02274 (0.845421_1.23726) |
| LRRC37A: rs2732703 , Chr17:46275856: T>G | |||||||||||
| Ancestry | EUR | AFR | AMR | EAS | SAS | MDE | AJ | FIN | AAC | CAS | CAH |
| A1 | G | G | G | G | G | G | G | G | G | G | G |
| P | 0.0159467 | 0.469114 | 0.499232 | NA | 0.765328 | 0.888089 | 0.141762 | 0.630329 | 0.722082 | 0.859343 | 0.603084 |
| OR (L95_U95) | 0.899139 (0.824667_0.980338) | 0.836562 (0.516022_1.35621) | 0.942435 (0.793531_1.11928) | NA | 0.915569 (0.513034_1.63394) | 0.841499 (0.0760695_9.30887) | 0.821482 (0.631937_1.06788) | 2.02936 (0.113665_36.2319) | 0.956198 (0.747062_1.22388) | 0.86174 (0.166199_4.4681) | 0.951874 (0.790384_1.14636) |
| r2_model <- lm(Protective/disease-modifying variant ~ APOESTATUS (ε3/ε3) +SEX + AGE + PC1 + PC2 + PC3 + PC4 + PC5, data = data) | |||||||||||
| 19q13.31: rs10423769, chr19:43100929:G>A | |||||||||||
| Ancestry | EUR | AFR | AMR | EAS | SAS | MDE | AJ | FIN | AAC | CAS | CAH |
| Multiple R-squared | 0.005739 | 0.007209 | 0.01396 | NA | NA | 0.08435 | 0.003222 | NA | 0.009795 | NA | 0.01382 |
| Adjusted R-squared | 0.00496 | 0.003815 | 0.01239 | NA | NA | −0.187 | −0.004857 | NA | 0.006832 | NA | 0.01093 |
| F-statistic | 7.369 | 2.124 | 8.924 | NA | NA | 0.3109 | 0.3988 | NA | 3.305 | NA | 4.776 |
| p-value (F-statistic) | 8.001e-10 | 0.03061 | 3.205e-12 | NA | NA | 0.9552 | 0.9215 | NA | 0.000918 | NA | 7.57e-06 |
| APOE :rs449647, Chr19:44905307: A>T | |||||||||||
| Ancestry | EUR | AFR | AMR | EAS | SAS | MDE | AJ | FIN | AAC | CAS | CAH |
| Multiple R-squared | 0.01708 | 0.0417 | 0.004391 | 0.09561 | 0.01963 | 0.1763 | 0.03854 | 0.557 | 0.03105 | 0.05191 | 0.01413 |
| Adjusted R-squared | 0.01631 | 0.03843 | 0.002812 | −0.007747 | 0.01642 | −0.06776 | 0.03074 | 0.3038 | 0.02815 | −0.001505 | 0.01124 |
| F-statistic | 22.18 | 12.73 | 2.781 | 0.925 | 6.122 | 0.7224 | 4.945 | 2.2 | 10.71 | 0.9718 | 4.885 |
| p-value (F-statistic) | < 2.2e-16 | < 2.2e-16 | 0.004543 | 0.5015 | 7.75e-08 | 0.6704 | 5.12e-06 | 0.09414 | 6.324e-15 | 0.4605 | 5.251e-06 |
| TOMM40 :rs11556505, Chr19:44892887: C>T | |||||||||||
| Ancestry | EUR | AFR | AMR | EAS | SAS | MDE | AJ | FIN | AAC | CAS | CAH |
| Multiple R-squared | 0.3606 | 0.007793 | 0.4079 | 0.3913 | 0.2386 | 0.542 | 0.3094 | 0.2094 | 0.02844 | 0.2733 | 0.1477 |
| Adjusted R-squared | 0.3601 | 0.004401 | 0.4069 | 0.3217 | 0.2361 | 0.4063 | 0.3038 | −0.2424 | 0.02554 | 0.2324 | 0.1452 |
| F-statistic | 720.1 | 2.297 | 434.3 | 5.625 | 95.83 | 3.994 | 55.26 | 0.4635 | 9.782 | 6.676 | 59.09 |
| p-value (F-statistic) | < 2.2e-16 | 0.01888 | < 2.2e-16 | 1.641e-05 | < 2.2e-16 | 0.003104 | < 2.2e-16 | 0.862 | 1.769e-13 | 2.122e-07 | < 2.2e-16 |
| AOCT:rs13116075 , Chr4:139008878: A>G | |||||||||||
| Ancestry | EUR | AFR | AMR | EAS | SAS | MDE | AJ | FIN | AAC | CAS | CAH |
| Multiple R-squared | 0.001859 | 0.003644 | 0.04211 | 0.111 | 0.01174 | 0.2214 | 0.01144 | 0.4719 | 0.02385 | 0.1566 | 0.007509 |
| Adjusted R-squared | 0.001077 | 0.0002378 | 0.04059 | 0.009412 | 0.008509 | −0.009359 | 0.003432 | 0.1701 | 0.02093 | 0.1091 | 0.004597 |
| F-statistic | 2.378 | 1.07 | 27.72 | 1.093 | 3.632 | 0.9594 | 1.428 | 1.564 | 8.162 | 3.297 | 2.579 |
| p-value (F-statistic) | 0.0148 | 0.3813 | < 2.2e-16 | 0.3787 | 0.000327 | 0.4869 | 0.1803 | 0.2219 | 5.824e-11 | 0.001752 | 0.008361 |
| CASS4 :rs6024870 , Chr20:56422512: G>A | |||||||||||
| Ancestry | EUR | AFR | AMR | EAS | SAS | MDE | AJ | FIN | AAC | CAS | CAH |
| Multiple R-squared | 0.005369 | 0.008078 | 0.04074 | NA | 0.003443 | 0.1515 | 0.00698 | NA | 0.001719 | 0.09891 | 0.006579 |
| Adjusted R-squared | 0.00459 | 0.004687 | 0.03922 | NA | 0.0001839 | −0.09995 | −0.001069 | NA | −0.001269 | 0.04814 | 0.003665 |
| F-statistic | 6.891 | 2.382 | 26.78 | NA | 1.056 | 0.6025 | 0.8672 | NA | 0.5753 | 1.948 | 2.258 |
| p-value (F-statistic) | 4.416e-09 | 0.01484 | < 2.2e-16 | NA | 0.391 | 0.7675 | 0.5438 | NA | 0.7989 | 0.05729 | 0.02107 |
| LRRC37A: rs2732703, Chr17:46275856: T>G | |||||||||||
| Ancestry | EUR | AFR | AMR | EAS | SAS | MDE | AJ | FIN | AAC | CAS | CAH |
| Multiple R-squared | 0.007884 | 0.03186 | 0.07655 | NA | 0.01582 | 0.3186 | 0.01161 | 0.3118 | 0.03262 | 0.03457 | 0.008172 |
| Adjusted R-squared | 0.007107 | 0.02855 | 0.07509 | NA | 0.0126 | 0.1167 | 0.003595 | −0.08138 | 0.02972 | −0.01982 | 0.005262 |
| F-statistic | 10.15 | 9.626 | 52.27 | NA | 4.915 | 1.578 | 1.449 | 0.793 | 11.27 | 0.6356 | 2.808 |
| p-value (F-statistic) | 3.267e-14 | 3.314e-13 | < 2.2e-16 | NA | 4.801e-06 | 0.178 | 0.172 | 0.6178 | 8.397e-16 | 0.7468 | 0.004226 |
| Interactionmodel <- glm(PHENO ~ Protective/disease-modifying variant * APOESTATUS (ε3/ε3) +SEX + AGE + PC1 + PC2 + PC3 + PC4 + PC5, data = data, family = binomial) | |||||||||||
| 19q13.31: rs10423769, chr19:43100929:G>A | |||||||||||
| Ancestry | EUR | AFR | AMR | EAS | SAS | MDE | AJ | FIN | AAC | CAS | CAH |
| P | −1.891e-01 | 1.515e-01 | −4.637e-02 | NA | NA | NA | −0.2460774 | NA | 0.0276379 | NA | −6.915e-02 |
| Std. Error | 3.283e-01 | 1.026e-01 | 2.072e-01 | NA | NA | NA | 0.3012184 | NA | 0.0948777 | NA | 1.294e-01 |
| z value | −0.576 | 1.476 | −0.224 | NA | NA | NA | −0.817 | NA | 0.291 | NA | −0.535 |
| p-value | 0.5647 | 0.139875 | 0.822920 | NA | NA | NA | 0.413963 | NA | 0.77082 | NA | 0.593 |
| APOE :rs449647, Chr19:44905307: A>T | |||||||||||
| Ancestry | EUR | AFR | AMR | EAS | SAS | MDE | AJ | FIN | AAC | CAS | CAH |
| P | 3.175e-01 | −1.109e-01 | 1.077e-01 | 0.32804 | 0.14264 | 9.32091 | 0.1583801 | −1.113e+01 | −0.0482250 | 0.237946 | −3.086e-03 |
| Std. Error | 4.275e-02 | 7.697e-02 | 6.468e-02 | 1.21693 | 0.18349 | 1470.20000 | 0.1127026 | 1.886e+05 | 0.0665037 | 0.473634 | 6.682e-02 |
| z value | 7.426 | −1.441 | 1.665 | 0.270 | 0.777 | 0.006 | 1.405 | 0.000 | −0.725 | 0.502 | −0.046 |
| p-value | 1.12e-13 | 0.149703 | 0.095932 | 0.787494 | 0.436955 | 0.9949 | 0.159935 | 1.000 | 0.46836 | 0.615398 | 0.963 |
| TOMM40 :rs11556505, Chr19:44892887: C>T | |||||||||||
| Ancestry | EUR | AFR | AMR | EAS | SAS | MDE | AJ | FIN | AAC | CAS | CAH |
| P | −3.407e-01 | −1.131e-01 | −3.658e-01 | −8.11183 | −0.1715 | 4.27063 | −0.3470659 | −1.898e+02 | −0.0667558 | −7.288818 | −2.756e-01 |
| Std. Error | 6.200e-02 | 1.187e-01 | 1.209e-01 | 986.15329 | 0.2004 | 1199.77469 | 0.1815237 | 1.617e+05 | 0.0960520 | 807.636366 | 1.044e-01 |
| z value | −5.495 | −0.953 | −3.026 | −0.008 | −0.856 | 0.004 | −1.912 | −0.001 | −0.695 | −0.009 | −2.639 |
| p-value | 3.92e-08 | 0.34073 | 0.002482 | 0.99344 | 0.392163 | 0.9972 | 0.05588 | 0.999 | 0.48706 | 0.992799 | 0.00831 |
| AOCT:rs13116075 , Chr4:139008878: A>G | |||||||||||
| Ancestry | EUR | AFR | AMR | EAS | SAS | MDE | AJ | FIN | AAC | CAS | CAH |
| P | 0.013728 | 4.872e-01 | −4.247e-02 | NA | −0.27401 | 1.38743 | 0.0965789 | −3033.5 | −0.1944697 | 4.893e-01 | 3.525e-02 |
| Std. Error | 0.041199 | 2.252e-01 | 9.446e-02 | NA | 0.21894 | 1.33996 | 0.1279155 | 435634.5 | 0.1258033 | 1.749e+03 | 9.380e-02 |
| z value | 0.333 | 2.164 | −0.450 | NA | −1.252 | 1.035 | 0.755 | −0.007 | −1.546 | 0.000 | 0.376 |
| p-value | 0.7390 | 0.030476 | 0.653013 | NA | 0.210747 | 0.3005 | 0.45024 | 0.994 | 0.122147 | 0.999777 | 0.707 |
| CASS4 :rs6024870 , Chr20:56422512: G>A | |||||||||||
| Ancestry | EUR | AFR | AMR | EAS | SAS | MDE | AJ | FIN | AAC | CAS | CAH |
| P | 8.275e-02 | 1.323e-01 | −6.875e-03 | NA | 0.47141 | 8.55974 | 0.0218776 | NA | −0.0635796 | 8.357e+00 | 1.233e-01 |
| Std. Error | 5.391e-02 | 1.266e-01 | 1.032e-01 | NA | 0.60405 | 1309.66064 | 0.1280412 | NA | 0.1009443 | 7.479e+02 | 9.777e-02 |
| z value | 1.535 | 1.045 | −0.067 | NA | 0.780 | 0.007 | 0.171 | NA | −0.630 | 0.011 | 1.261 |
| p-value | 0.1248 | 0.296074 | 0.946866 | NA | 0.435140 | 0.9948 | 0.864331 | NA | 0.52879 | 0.991085 | 0.207 |
| LRRC37A: rs2732703, Chr17:46275856: T>G | |||||||||||
| Ancestry | EUR | AFR | AMR | EAS | SAS | MDE | AJ | FIN | AAC | CAS | CAH |
| P | 2.905e-02 | 2.406e-01 | −2.053e-01 | NA | 0.1459 | −0.35985 | 0.0223262 | NA | 0.0386594 | −0.418667 | −1.656e-02 |
| Std. Error | 4.379e-02 | 2.542e-01 | 8.825e-02 | NA | 0.3104 | 1.29242 | 0.1328074 | NA | 0.1275317 | 0.865756 | 9.532e-02 |
| z value | 0.663 | 0.946 | −2.327 | NA | 0.470 | −0.278 | 0.168 | NA | 0.303 | −0.484 | −0.174 |
| p-value | 0.5071 | 0.34390 | 0.019977 | NA | 0.638221 | 0.7807 | 0.86650 | NA | 0.7618 | 0.628680 | 0.862 |
ASP, Alzheimer’s Disease Sequencing Project; EUR, European; AFR, African; AMR, American Admixed; AAC,African Admixed; AJ, Ashkenazi Jewish; CAS, Central Asian; EAS, Eastern Asian; SAS, South Asian; MDE, Middle Eastern; FIN, Finnish; CAH, Complex Admixture History; NA, Not available