Identification of Novel Candidate Genes for Alzheimer's Disease by ...

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cCenter for Human Genetics, Boston University School of Medicine, Boston, MA, USA ... iDepartment of Neurology, University of Louisville, Louisville, KY, USA.
Journal of Alzheimer’s Disease 23 (2011) 1–7 IOS Press

Supplementary Data

Identification of Novel Candidate Genes for Alzheimer’s Disease by Autozygosity Mapping using Genome Wide SNP Data Richard Shervaa , Clinton T. Baldwina,c , Rivka Inzelbergd , Badri Vardarajana , L. Adrienne Cupplese , Kathryn Lunettae , Abdalla Bowirratg , Adam Najh , Margaret Pericak-Vanceh , Robert P. Friedlandi and Lindsay A. Farrera,b,e,f,∗ a Department

of Medicine (Genetics Program), Boston University School of Medicine, Boston, MA, USA of Neurology, Ophthalmology, and Genetics & Genomics, Boston University School of Medicine, Boston, MA, USA c Center for Human Genetics, Boston University School of Medicine, Boston, MA, USA d Sagol Neuroscience Center, Department of Neurology, Sheba Medical Center, Tel Hashomer and Sackler, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel e Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA f Department of Epidemiology, Boston University School of Public Health, Boston, MA, USA g Ziv Medical Center, Safed, Israel h John P. Hussman Institute for Human Genomics, University of Miami Milller School of Medicine, Miami, FL, USA i Department of Neurology, University of Louisville, Louisville, KY, USA b Departments

Handling Associate Editor: Alan Lerner

Accepted 1 October 2010

∗ Correspondence to: Lindsay A. Farrer, Boston University School of Medicine, Genetics L-320, 72 East Concord Street, Boston, MA 02118, USA. Tel.: +1 617 638 5393; Fax: +1 617 638 4275; E-mail: [email protected].

ISSN 1387-2877/11/$27.50 © 2011 – IOS Press and the authors. All rights reserved

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2

R. Sherva et al. / AD GWAS in a Genetically Isolated Population Supplementary Table S1 SNPs in homozygous regions associated with AD in Wadi Ara at p ≤ 0.05

Chr

SNP

2 2 2 2 2 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 8 8 8 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9

rs1872788 rs901530 rs6753844 rs4671432 rs1014119 rs537160 rs12333245 rs1009382 rs2269429 rs9469079 rs9469080 rs3749962 rs9469082 rs3130286 rs204877 rs169496 rs3134950 rs1061808 rs3130283* rs2269423 rs3134943 rs1800684 rs1044506 rs3131294 rs396960 rs13271711 rs10089053 rs4424286 rs10868248 rs7863165 rs10735572 rs7037671 rs4574911 rs1027284 rs10868358 rs4744583 rs870011 rs953372 rs4418399 rs4403478 rs7035415 rs7863229 rs7859880 rs755778 rs2997657 rs12352964 rs3015237 rs4744970 rs4744972 rs3015239 rs7035878 rs11141566 rs4237238 rs12341763 rs4237239 rs6559970 rs1927107 rs4744979 rs7853094 rs12349576 rs4744983

Position

MAF case

MAF control

OR

p

Quality

Gene

Type

62671182 62671771 62673907 62676846 62678986 32024379 32127747 32134085 32137161 32140399 32143405 32144335 32148909 32150300 32155414 32160961 32235455 32244525 32246523 32253685 32255739 32259972 32280043 32288124 32299559 49526732 49660586 49671053 71703997 71764547 71765581 71766818 71797023 71799485 71801500 71801754 71804632 71805689 71806161 71806885 71808349 71808783 71843256 71850379 71852509 71856948 71859460 71861470 71861846 71862722 71875979 71885934 71900383 71900928 71903716 71917562 71918553 71922475 71925881 71927401 71949873

0.35 0.35 0.35 0.34 0.33 0.12 0.19 0.25 0.19 0.18 0.19 0.19 0.19 0.17 0.19 0.19 0.34 0.33 0.11 0.32 0.10 0.09 0.08 0.10 0.28 0.04 0.08 0.08 0.12 0.18 0.06 0.06 0.17 0.17 0.17 0.17 0.17 0.17 0.17 0.17 0.17 0.17 0.20 0.19 0.19 0.09 0.13 0.13 0.13 0.11 0.13 0.14 0.14 0.11 0.14 0.15 0.15 0.15 0.15 0.15 0.11

0.44 0.44 0.44 0.43 0.43 0.06 0.26 0.18 0.26 0.25 0.26 0.26 0.26 0.12 0.26 0.26 0.26 0.26 0.06 0.24 0.04 0.03 0.04 0.05 0.36 0.07 0.06 0.06 0.07 0.11 0.04 0.04 0.10 0.10 0.10 0.10 0.10 0.10 0.10 0.11 0.10 0.10 0.27 0.26 0.26 0.14 0.20 0.20 0.20 0.16 0.20 0.20 0.20 0.17 0.21 0.21 0.21 0.21 0.21 0.21 0.17

0.60 0.60 0.60 0.61 0.61 2.37 0.59 1.77 0.59 0.58 0.60 0.60 0.60 1.87 0.61 0.61 1.63 1.66 3.13 1.67 3.66 4.36 3.73 2.82 0.61 0.24 3.25 3.86 2.66 2.07 3.32 3.32 2.42 2.42 2.42 2.42 2.42 2.42 2.42 2.33 2.42 2.42 0.55 0.59 0.59 0.41 0.57 0.57 0.57 0.51 0.57 0.61 0.61 0.52 0.61 0.61 0.61 0.60 0.60 0.60 0.52

0.04 0.04 0.04 0.04 0.04 0.03 0.02 0.03 0.02 0.02 0.03 0.03 0.03 0.05 0.03 0.03 0.03 0.02 0.004 0.02 0.002 0.002 0.03 0.04 0.03 0.04 0.05 0.03 0.01 0.01 0.03 0.03 0.005 0.005 0.005 0.005 0.005 0.005 0.005 0.007 0.005 0.005 0.02 0.03 0.03 0.01 0.02 0.02 0.02 0.02 0.02 0.04 0.04 0.01 0.03 0.03 0.03 0.03 0.03 0.03 0.01

0.88 0.88 0.88 0.89 0.90 0.98 1.00 0.94 1.00 0.99 1.00 1.00 1.00 0.95 1.00 1.00 0.92 0.91 0.96 0.96 1.00 0.98 0.96 0.93 0.92 0.92 0.89 0.90 0.99 0.98 0.95 0.95 1.00 1.00 1.00 1.00 1.00 1.00 1.00 0.98 1.00 1.00 0.90 0.93 0.93 0.92 1.00 1.00 1.00 0.96 1.00 1.00 1.00 1.00 0.99 1.00 1.00 1.00 1.00 1.00 0.99

NA NA NA NA NA CFB TNXB TNXB TNXB TNXB TNXB TNXB TNXB TNXB TNXB TNXB PPT2 AGPAT1 AGPAT1 AGPAT1 RNF5 AGER NOTCH4 NOTCH4 NOTCH4 NA NA NA C9orf135 NA NA NA NA NA NA NA NA NA NA NA NA NA NA MAMDC2 MAMDC2 MAMDC2 MAMDC2 MAMDC2 MAMDC2 MAMDC2 MAMDC2 MAMDC2 MAMDC2 MAMDC2 MAMDC2 MAMDC2 MAMDC2 MAMDC2 MAMDC2 MAMDC2 MAMDC2

NA NA NA NA NA intron intron missense missense intron intron synonymous intron intron intron intron intron 3 UTR intron intron intron synonymous synonymous intron intron NA NA NA intron NA NA NA NA NA NA NA NA NA NA NA NA NA NA intron intron intron intron intron intron intron intron intron intron intron intron intron intron intron intron intron intron

R. Sherva et al. / AD GWAS in a Genetically Isolated Population

3

Supplementary Table S1 Continued Chr

SNP

9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 15 15

rs10868610 rs11794396 rs11142019 rs2148856 rs11142141 rs7873075 rs1180085 rs1180109 rs1180116 rs10868798 rs1180131 rs11142355 rs7849942 rs12346675 rs7847861 rs12684881 rs4745006 rs7875663 rs7849735 rs6560138 rs3923700 rs3923699 rs3901151 rs7018675 rs10868838 rs4472581 rs10868839 rs6560139 rs7856642 rs11792173 rs9969768 rs7847938 rs7024178 rs7871523 rs10868840 rs10868841 rs10868843 rs7032346 rs10868845 rs7037072 rs10780936 rs4744600 rs10868854 rs10780951 rs11142509 rs7027906 rs11142539 rs4131069 rs4540466 rs1011308 rs7874138 rs12378618 rs12344255 rs11638769 rs1256841

Position

MAF case

MAF control

OR

p

Quality

Gene

Type

71954693 71992354 71992659 72001259 72020229 72034009 72057147 72075087 72087254 72092323 72095224 72100553 72122702 72147361 72162634 72167165 72175706 72289023 72289274 72289908 72292598 72292644 72292961 72293046 72294131 72294703 72294896 72295317 72296173 72298171 72300708 72300995 72302374 72304099 72304518 72308484 72309535 72309852 72310966 72311118 72311143 72337348 72383191 72383357 72423141 72471178 72474803 72475275 72477527 72478076 72485540 72496209 72497811 86659786 88349309

0.11 0.11 0.11 0.11 0.11 0.11 0.11 0.10 0.11 0.11 0.11 0.11 0.11 0.11 0.11 0.11 0.15 0.44 0.48 0.48 0.48 0.44 0.48 0.48 0.25 0.48 0.25 0.48 0.49 0.49 0.50 0.50 0.26 0.50 0.26 0.26 0.50 0.50 0.26 0.50 0.26 0.30 0.42 0.42 0.20 0.26 0.26 0.26 0.25 0.26 0.26 0.22 0.24 0.09 0.05

0.17 0.17 0.17 0.17 0.17 0.17 0.17 0.17 0.17 0.17 0.17 0.17 0.16 0.17 0.16 0.16 0.20 0.33 0.38 0.38 0.38 0.33 0.38 0.38 0.18 0.38 0.18 0.38 0.38 0.38 0.39 0.39 0.18 0.39 0.18 0.18 0.39 0.39 0.18 0.39 0.18 0.22 0.33 0.33 0.14 0.18 0.18 0.18 0.18 0.18 0.18 0.15 0.17 0.12 0.08

0.52 0.52 0.52 0.52 0.52 0.52 0.52 0.53 0.54 0.54 0.54 0.54 0.55 0.56 0.58 0.59 0.56 1.77 1.55 1.55 1.56 1.77 1.56 1.56 1.53 1.56 1.53 1.56 1.56 1.54 1.54 1.54 1.53 1.53 1.53 1.53 1.53 1.53 1.56 1.53 1.57 1.62 1.50 1.49 1.83 1.65 1.65 1.65 1.66 1.64 1.63 1.76 1.66 0.30 0.44

0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.02 0.02 0.02 0.02 0.03 0.02 0.03 0.03 0.04 0.005 0.02 0.02 0.02 0.00 0.02 0.02 0.04 0.02 0.04 0.02 0.02 0.03 0.03 0.03 0.04 0.03 0.04 0.04 0.03 0.03 0.04 0.03 0.04 0.02 0.03 0.03 0.05 0.04 0.04 0.04 0.04 0.04 0.04 0.04 0.05 0.03 0.02

0.99 0.99 0.99 0.99 0.99 0.99 0.99 1.00 1.00 0.99 1.00 1.00 0.99 0.99 1.00 1.00 0.90 0.97 0.99 0.99 1.00 0.97 1.00 1.00 0.97 0.98 0.97 0.98 0.98 0.97 0.98 0.98 0.98 0.98 0.98 0.98 0.98 0.98 0.97 0.98 0.96 0.93 1.00 0.99 0.93 0.99 1.00 1.00 0.99 1.00 1.00 0.98 0.97 0.81 1.00

MAMDC2 MAMDC2 MAMDC2 MAMDC2 MAMDC2 NA NA SMC5 SMC5 SMC5 SMC5 SMC5 SMC5 SMC5 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA TRPM3 TRPM3 TRPM3 TRPM3 TRPM3 TRPM3 TRPM3 TRPM3 TRPM3 TRPM3 TRPM3 NA ZNF710

intron intron intron intron intron NA NA intron missense intron intron intron intron intron NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA intron intron intron intron intron intron intron intron intron intron intron NA intron

*SNPs were nominally associated with AD in the meta-analysis, OR = odds ratio, Quality = the posterior probability of a correctly imputed genotype.

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R. Sherva et al. / AD GWAS in a Genetically Isolated Population Supplementary Table S2 SNPs associated with AD at p < 10−4 in Wadi Ara

Chr

SNP

1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 3 3 3 3 3 3 3 3 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 5 5 6 6 6 6 6 6 6 6 6

rs4457599 rs4539154 rs2068611 rs4907035 rs12127377 rs1553450 rs11102707 rs12129050 rs11102709 rs10108 rs12032159 rs2124328 rs2791559 rs741472 rs2593708 rs7621429 rs4245886 rs7636660 rs4572808 rs7644602 rs11708149 rs6783478 rs4955274 rs6853435 rs3810765 rs1456389 rs7667718 rs10006749 rs1902467 rs11723258 rs7680824 rs1456401 rs10031057 rs7682762 rs7682436 rs13139425 rs13119833 rs13101315 rs5018782 rs5018783 rs5018784 rs5018785 rs2405206 rs1598633 rs7680792 rs4401438 rs4513550 rs6823476 rs897612 rs12509282 rs2410936 rs13357822 rs4946727 rs7761791 rs6903903 rs17514051 rs7770777 rs12198667 rs7753492 rs12192420 rs11751945

BP

MAF case

MAF control

OR

p

Quality

Gene

SNP type

83885479 83885747 83886234 83887487 114291496 114292303 114295106 114298130 114313606 114317853 217653038 217654860 217655426 71290362 134695885 32277533 32279107 32287918 32292718 32295412 32296603 32297979 32302425 154925466 154928930 154933566 154951092 154951278 154951578 154952520 154953085 154953422 154966256 154978052 154978117 154979129 154980346 154980735 154981386 154981427 154981437 154981510 154982258 154982287 154983049 154984644 154984743 154984784 154984867 154986084 106501648 167134292 106680065 106683679 106684200 119576443 119593904 119605859 119606742 119607599 119614780

0.52 0.52 0.52 0.29 0.29 0.29 0.29 0.30 0.29 0.29 0.30 0.30 0.37 0.21 0.40 0.46 0.46 0.44 0.43 0.45 0.49 0.49 0.45 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.51 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.49 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.06 0.05 0.21 0.45 0.45 0.29 0.29 0.29 0.29 0.29 0.29

0.40 0.40 0.40 0.47 0.17 0.17 0.17 0.18 0.17 0.17 0.17 0.17 0.23 0.36 0.55 0.31 0.31 0.28 0.27 0.29 0.32 0.32 0.29 0.35 0.35 0.35 0.35 0.35 0.35 0.35 0.36 0.35 0.36 0.37 0.36 0.36 0.36 0.37 0.36 0.36 0.36 0.62 0.36 0.36 0.36 0.36 0.36 0.36 0.36 0.37 0.15 0.10 0.07 0.25 0.26 0.15 0.14 0.14 0.14 0.14 0.14

2.77 2.77 2.78 0.25 2.78 2.86 2.89 0.35 2.96 2.86 2.99 2.99 2.86 0.44 0.39 2.57 2.56 2.78 2.86 2.61 2.58 2.60 3.07 2.32 2.32 2.31 2.33 2.33 2.33 2.33 2.47 2.33 2.35 2.45 2.38 2.38 2.38 2.40 2.38 2.38 2.38 0.41 2.38 2.38 2.38 2.39 2.39 2.39 2.39 2.39 0.27 0.17 0.27 2.36 0.41 2.79 2.71 0.37 0.37 0.37 0.37

1.77E-05 1.76E-05 1.75E-05 2.74E-07 8.89E-05 8.03E-05 7.90E-05 8.06E-05 7.36E-05 7.23E-05 5.46E-05 5.07E-05 2.52E-05 8.13E-05 2.79E-05 5.66E-05 5.52E-05 1.82E-05 1.82E-05 2.28E-05 2.47E-05 2.46E-05 1.02E-05 4.46E-05 4.47E-05 4.50E-05 4.87E-05 4.87E-05 4.88E-05 4.90E-05 3.11E-05 4.90E-05 5.21E-05 4.03E-05 5.86E-05 5.92E-05 5.95E-05 6.08E-05 5.96E-05 5.99E-05 6.04E-05 6.51E-05 6.09E-05 6.13E-05 6.14E-05 6.26E-05 6.32E-05 6.33E-05 6.37E-05 6.44E-05 8.90E-05 5.41E-05 2.88E-05 1.73E-05 1.87E-05 7.78E-05 7.40E-05 7.39E-05 7.39E-05 7.18E-05 6.75E-05

0.87 0.87 0.87 0.83 0.95 0.94 0.93 0.92 0.92 0.92 0.96 0.97 0.99 1.00 0.86 0.89 0.89 0.90 0.88 0.94 0.92 0.91 0.84 0.95 0.95 0.96 0.94 0.94 0.94 0.94 0.89 0.94 0.93 0.89 0.91 0.91 0.91 0.89 0.91 0.91 0.90 0.88 0.90 0.90 0.90 0.90 0.90 0.90 0.90 0.90 1.00 0.95 0.99 1.00 0.97 0.98 1.00 1.00 1.00 1.00 1.00

NA NA NA NA HIPK1 HIPK1 HIPK1 HIPK1 HIPK1 HIPK1 NA NA NA PAIP2B NA CMTM8 CMTM8 CMTM8 CMTM8 CMTM8 CMTM8 CMTM8 CMTM8 SFRP2 SFRP2 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA ODZ2 NA NA NA MAN1A1 MAN1A1 MAN1A1 MAN1A1 MAN1A1 MAN1A1

NA NA NA NA intron intron intron intron intron 3 UTR NA NA NA intron NA intron intron intron intron intron intron intron intron intron intron NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA intron NA NA NA intron intron intron intron intron intron

R. Sherva et al. / AD GWAS in a Genetically Isolated Population

5

Supplementary Table S2 Continued Chr

SNP

6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 7 7 7 8 8 8 9 9 9 9 9 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 11 11 12

rs7740993 rs11153800 rs12205826 rs11153803 rs11153805 rs1022869 rs7760582 rs6909928 rs7743824 rs10457352 rs11153808 rs10457353 rs11759899 rs6913654 rs10485001 rs7767198 rs12205260 rs10456921 rs11153812 rs11962938 rs10872177 rs6920832 rs9489697 rs6936790 rs6569076 rs6904915 rs12527248 rs2036257 rs3887627 rs3931139* rs7780678* rs10957176 rs1525053 rs7463918 rs1006116 rs10982662 rs10982663 rs10983328 rs7028544 rs17101073 rs11814517 rs17101125 rs10509462 rs17101130 rs7069185 rs17101139 rs11815363 rs11816685 rs11819041 rs17101164 rs999799 rs17101193 rs17101196 rs7909420 rs17101209 rs17101227 rs12570609 rs7914006 rs10832683 rs7103236 rs736107

BP

MAF case

MAF control

OR

p

Quality

Gene

SNP type

119616700 119622517 119628503 119632568 119653359 119655780 119659056 119659906 119662926 119665757 119667753 119668056 119670815 119672875 119675324 119675888 119677438 119679026 119679931 119682759 119684399 119730755 119741223 119749117 119751989 119780447 119789297 119801100 57282944 138093331 138103892 62069205 69296139 113473777 110381485 117104713 117106399 118530159 118530393 84669660 84681945 84683470 84688185 84688446 84706503 84708657 84712638 84712859 84724809 84727384 84728972 84734906 84735020 84741572 84745160 84757598 129058140 129059422 16790037 42018659 12518677

0.29 0.30 0.30 0.30 0.30 0.30 0.30 0.30 0.30 0.30 0.30 0.30 0.30 0.30 0.30 0.30 0.30 0.30 0.30 0.30 0.30 0.23 0.38 0.39 0.39 0.39 0.39 0.39 0.35 0.37 0.40 0.12 0.18 0.17 0.32 0.21 0.21 0.18 0.26 0.11 0.11 0.11 0.11 0.11 0.11 0.11 0.11 0.11 0.12 0.12 0.12 0.12 0.12 0.12 0.12 0.12 0.45 0.44 0.29 0.05 0.06

0.14 0.15 0.15 0.15 0.15 0.15 0.15 0.15 0.15 0.14 0.14 0.14 0.14 0.14 0.14 0.14 0.14 0.14 0.14 0.14 0.14 0.12 0.24 0.24 0.24 0.24 0.24 0.24 0.21 0.23 0.26 0.20 0.08 0.30 0.46 0.29 0.29 0.32 0.44 0.03 0.03 0.03 0.03 0.03 0.03 0.03 0.03 0.03 0.03 0.03 0.03 0.03 0.03 0.03 0.03 0.03 0.31 0.31 0.20 0.08 0.02

0.36 2.80 2.75 2.70 2.70 2.70 2.70 2.71 2.71 0.37 0.37 0.36 0.36 2.75 2.75 2.75 2.75 2.74 2.74 2.74 0.37 0.28 0.39 0.39 0.39 2.53 0.40 0.40 2.49 2.50 2.54 0.25 0.22 0.34 0.42 0.30 0.30 0.32 0.39 0.20 0.22 4.56 0.22 4.61 0.21 0.21 4.79 4.79 4.84 0.21 4.83 4.83 0.21 0.21 0.21 0.22 2.46 2.42 3.92 0.16 47.83

6.58E-05 4.40E-05 4.58E-05 5.28E-05 5.16E-05 5.13E-05 5.07E-05 5.05E-05 5.00E-05 4.76E-05 4.69E-05 4.67E-05 4.63E-05 4.62E-05 4.64E-05 4.68E-05 4.71E-05 4.77E-05 4.82E-05 5.02E-05 5.04E-05 4.91E-05 5.66E-05 5.10E-05 5.13E-05 5.62E-05 5.73E-05 5.78E-05 2.73E-05 8.28E-05 2.11E-05 6.60E-05 5.61E-05 5.83E-05 8.26E-05 8.33E-05 8.34E-05 6.72E-05 6.63E-05 8.36E-05 5.67E-05 5.45E-05 4.35E-05 4.31E-05 2.31E-05 2.28E-05 2.25E-05 2.23E-05 1.85E-05 1.70E-05 1.61E-05 1.62E-05 1.62E-05 1.63E-05 1.63E-05 1.80E-05 1.75E-05 2.44E-05 6.55E-05 7.59E-05 3.37E-06

1.00 0.99 0.99 0.99 0.99 0.99 0.99 0.99 0.99 0.99 0.99 0.99 0.99 0.99 0.99 0.99 0.99 0.99 0.99 0.99 0.99 0.90 0.98 0.99 0.99 0.99 0.99 0.99 0.97 0.92 0.98 0.86 0.91 0.93 0.99 0.82 0.82 0.86 1.00 0.98 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 0.99 0.93 0.93 0.73 0.95 0.94

MAN1A1 MAN1A1 MAN1A1 MAN1A1 MAN1A1 MAN1A1 MAN1A1 MAN1A1 MAN1A1 MAN1A1 MAN1A1 MAN1A1 MAN1A1 MAN1A1 MAN1A1 MAN1A1 MAN1A1 MAN1A1 MAN1A1 MAN1A1 MAN1A1 NA NA NA NA NA NA NA NA ATP6V0A4 ATP6V0A4 NA DEPDC2 CSMD3 NA 1-Dec 1-Dec ASTN2 ASTN2 NRG3 NRG3 NRG3 NRG3 NRG3 NRG3 NRG3 NRG3 NRG3 NRG3 NRG3 NRG3 NRG3 NRG3 NA NA NA DOCK1 DOCK1 PLEKHA7 NA NA

intron intron intron intron intron intron intron intron intron intron intron intron intron intron intron intron intron intron intron intron intron NA NA NA NA NA NA NA NA intron intron NA intron intron NA intron intron intron intron intron intron intron intron intron intron intron intron intron intron intron intron missense synonymous NA NA NA intron intron intron NA NA

6

R. Sherva et al. / AD GWAS in a Genetically Isolated Population Supplementary Table S2 Continued

Chr

SNP

12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 13 13 13 13 13 13 13 14 14 14 14 14 14 14 14 14 14

rs2287539 rs1862013 rs7296684 rs2032762 rs12424762 rs12425010 rs12422226 rs7310514 rs12423659 rs1021257 rs12230422 rs10876062 rs826837 rs826836 rs7309194 rs12424244 rs17126713 rs9943730 rs12425783 rs12422883 rs10876185 rs11169878 rs7311812 rs7308580 rs7307936 rs1516555 rs12423647 rs1878224 rs7968397 rs7971601 rs7974510 rs1878223 rs7298320 rs12424948 rs7294592 rs11180823 rs12297524 rs11059603 rs12299465* rs11609257* rs12825406 rs1514898 rs1193373 rs1193376* rs9603150 rs9315475 rs10219784 rs1980733 rs1980732 rs1324020 rs9532392 rs10142046 rs11625679* rs12587303 rs17780651 rs2042045 rs3815626 rs2363641 rs2111699 rs2363643 rs4147578

BP

MAF case

MAF control

OR

p

Quality

Gene

SNP type

14585501 14586144 14598395 14599040 36929753 36970274 37042040 37053411 37265907 37425785 37447314 37454453 37470792 37471673 37494213 37501919 37505285 37529460 37536951 37543217 37544916 37551227 37568585 37571225 37571373 37583295 37593034 37595981 37596858 37596918 37596997 37599402 37604104 37605219 74751512 74764208 127302475 127302970 127303503 127303699 127304152 127304208 127311708 127312068 36693584 36696434 36710511 36714086 36714223 36720869 38998591 72117717 72118095 72128367 72131479 76837731 76840587 76852887 76858350 76858661 76860169

0.15 0.15 0.15 0.15 0.06 0.06 0.06 0.06 0.07 0.08 0.12 0.18 0.19 0.19 0.19 0.19 0.19 0.19 0.19 0.19 0.19 0.20 0.08 0.15 0.15 0.15 0.14 0.14 0.14 0.14 0.14 0.14 0.14 0.14 0.20 0.23 0.36 0.36 0.34 0.36 0.36 0.36 0.25 0.25 0.24 0.24 0.23 0.23 0.23 0.23 0.14 0.17 0.17 0.19 0.14 0.28 0.29 0.29 0.28 0.29 0.22

0.26 0.26 0.26 0.26 0.01 0.01 0.01 0.01 0.01 0.02 0.04 0.07 0.09 0.09 0.08 0.08 0.08 0.08 0.08 0.08 0.08 0.09 0.02 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.06 0.05 0.31 0.33 0.19 0.19 0.19 0.19 0.19 0.19 0.40 0.40 0.13 0.13 0.12 0.13 0.12 0.13 0.05 0.09 0.09 0.09 0.06 0.14 0.15 0.15 0.15 0.15 0.10

0.36 0.37 0.36 0.36 0.03 0.03 0.03 27.77 0.05 0.06 0.19 4.28 0.26 3.82 3.87 0.25 3.94 0.25 4.04 4.03 0.25 3.37 0.09 0.18 5.60 5.55 5.17 5.12 0.21 4.73 4.72 0.22 0.23 0.22 0.32 0.31 0.40 2.51 0.37 0.40 2.52 2.53 0.44 0.44 0.33 3.05 0.35 0.35 2.89 0.35 0.24 4.05 0.25 3.57 0.14 2.71 0.36 0.36 0.36 2.70 3.08

6.66E-05 6.68E-05 6.40E-05 6.30E-05 5.27E-05 4.17E-05 3.50E-05 3.39E-05 2.60E-05 9.49E-06 8.84E-05 4.23E-05 6.01E-05 5.96E-05 5.05E-05 3.47E-05 3.32E-05 3.01E-05 2.88E-05 2.93E-05 2.90E-05 7.86E-05 6.35E-05 1.42E-05 1.42E-05 1.45E-05 2.16E-05 2.34E-05 3.70E-05 3.77E-05 3.83E-05 4.30E-05 6.67E-05 4.68E-05 5.73E-05 5.42E-05 6.16E-05 6.04E-05 7.50E-05 5.74E-05 5.68E-05 5.62E-05 2.86E-05 2.86E-05 5.17E-05 5.02E-05 7.30E-05 7.88E-05 7.46E-05 7.48E-05 8.86E-05 8.33E-05 7.60E-05 4.44E-05 3.23E-06 8.98E-05 5.05E-05 5.00E-05 5.28E-05 5.60E-05 5.34E-05

1.00 1.00 0.99 0.99 0.97 0.97 0.97 0.97 0.98 0.98 0.98 0.98 0.98 0.98 0.98 0.99 0.99 0.98 0.98 0.98 0.98 1.00 0.98 0.99 0.99 0.99 1.00 1.00 0.99 0.99 0.99 0.99 0.98 0.99 0.82 0.79 0.96 0.96 0.90 0.96 0.96 0.96 1.00 0.99 0.97 0.97 0.99 0.99 0.99 0.99 0.99 0.91 0.92 0.95 0.91 0.96 0.93 0.93 0.93 0.94 0.96

FLJ22662 FLJ22662 FLJ22662 FLJ22662 NA NA NA NA NA CPNE8 CPNE8 CPNE8 CPNE8 CPNE8 CPNE8 CPNE8 CPNE8 CPNE8 CPNE8 CPNE8 CPNE8 CPNE8 CPNE8 CPNE8 CPNE8 CPNE8 NA NA NA NA NA NA NA NA NAP1L1 NAP1L1 NA TMEM132C TMEM132C TMEM132C TMEM132C TMEM132C TMEM132C NA NA NA NA NA NA NA LHFP NA NA NA NA POMT2 POMT2 POMT2 GSTZ1 GSTZ1 GSTZ1

intron intron intron intron NA NA NA NA NA intron intron intron intron intron intron intron intron intron intron intron intron intron intron intron intron intron NA NA NA NA NA NA NA NA intron intron NA promoter promoter promoter promoter promoter promoter NA NA NA NA NA NA NA intron NA NA NA NA intron intron intron intron 5 UTR intron

R. Sherva et al. / AD GWAS in a Genetically Isolated Population

7

Supplementary Table S2 Continued Chr

SNP

14 14 14 17 17 17 17 17 19 19 19 20 20 20 20 20 20 20 20 20 20 22 22 22 22 22

rs8016187 rs2287395 rs2270423 rs2750012* rs11658079 rs9915388 rs7215435 rs16951470 rs1368445 rs11084710 rs10407579 rs2300186 rs2300185 rs6074191 rs4813945 rs6134051 rs2072965 rs4813044 rs3746814 rs6040293 rs7273511 rs2187898 rs5761859 rs5761860 rs5752451 rs5761863

BP

MAF case

MAF control

OR

p

Quality

Gene

SNP type

76860625 76861272 76865391 631011 639270 644926 645414 15263319 35601575 38344196 38345252 1082900 1083413 1084156 1084656 1085204 1094136 1096783 1100237 1101225 8446416 25676779 25677402 25677493 25678321 25678456

0.22 0.22 0.22 0.14 0.15 0.13 0.14 0.12 0.08 0.48 0.48 0.33 0.34 0.31 0.34 0.34 0.30 0.34 0.33 0.30 0.25 0.36 0.36 0.36 0.36 0.36

0.10 0.10 0.10 0.07 0.07 0.07 0.09 0.08 0.03 0.30 0.30 0.48 0.49 0.47 0.49 0.50 0.46 0.50 0.49 0.46 0.37 0.20 0.20 0.20 0.20 0.20

3.01 0.35 2.86 0.18 5.36 9.46 0.09 15.46 0.08 2.43 0.41 0.41 0.42 0.41 0.42 0.43 0.41 0.44 0.43 0.42 0.33 0.40 0.40 2.49 2.49 2.49

4.72E-05 5.49E-05 5.53E-05 7.25E-05 4.93E-05 4.47E-05 3.43E-05 3.93E-05 3.04E-05 1.85E-05 1.89E-05 1.76E-05 2.27E-05 1.73E-05 2.27E-05 2.28E-05 1.17E-05 1.92E-05 2.07E-05 2.18E-05 8.01E-05 6.89E-05 6.89E-05 6.89E-05 6.91E-05 6.86E-05

0.97 1.00 1.00 0.92 0.91 0.86 0.83 0.85 0.93 0.98 0.98 0.92 0.94 0.91 0.95 0.97 0.92 0.98 0.95 0.91 0.88 0.99 0.99 0.99 0.99 0.99

GSTZ1 GSTZ1 GSTZ1 GLOD4 RNMTL1 NA NA NA ZNF536 WDR88 WDR88 PSMF1 PSMF1 PSMF1 PSMF1 PSMF1 PSMF1 PSMF1 NA NA PLCB1 NA NA NA NA NA

intron intron intron intron intron NA NA NA intron intron intron intron intron intron intron intron 3 UTR 3 NA NA intron NA NA NA NA NA

*SNP was nominally associated with AD in the meta-analysis, OR = odds ratio, Quality = the posterior probability of a correctly imputed genotype.