Table S3: Risk allele frequencies for rs11385942 and rs657152 for six external and study independent

TOPMed-impute

STUDY_CASES
STUDY_CONTROLS
EXTERNAL_CONTROLS
GENOTYPING_PLATFORM
N_QCED
BATCH
SNP
A1
A2
A1F_cases
A1F_ctrs
GENO_HOM_A1
GENO_HET
GENO_HOM_A2
IMP_STATUS
IMP_R2
r rs11385942 and rs657152 for six external and study independent TOPMed-imputed Spanish and Italian population-based GWAS

GWAS data sets of cases included in analysis I (see Supplementary Methods for case panels and analysis strategy)
GWAS data sets of controls included in analysis I (see Supplementary Methods for control panels and analysis strategy)
GWAS data sets of controls from different Illumina and Affymetrix (i.e. non-Illumina GSA) genotyping platforms.
Type of SNP array
Number of genotyped DNA samples after quality control (QC)
Name of contributing center
SNP ID as reported in TOPMed imputation reference panel
Minor and risk allele
Major allele
Allele frequency of minor/risk allele 1 in cases
Allele frequency of minor/risk allele 1 in controls
Homozygous genotype frequency for allele 1
Heterozygous genotype frequency
Homozygous genotype frequency for allele 2
Genotypes genotyped or TOPMed imputed
TOPMed imputation quality score
 Table S3
Table S3: Risk allele frequencies for rs11385942 and rs657152 for six external and study independent TOPMed-im

STUDYTYPE COUNTRY GENOTYPING_PLATFORM N_QCED

STUDY_CASES SPAIN Illumina Global Screening Array (GSA) 301
STUDY_CASES SPAIN Illumina Global Screening Array (GSA) 45
STUDY_CASES SPAIN Illumina Global Screening Array (GSA) 201
STUDY_CASES SPAIN Illumina Global Screening Array (GSA) 228
STUDY_CONTROLS SPAIN Illumina Global Screening Array (GSA) 950
STUDY_CASES ITALY Illumina Global Screening Array (GSA) 503
STUDY_CASES ITALY Illumina Global Screening Array (GSA) 192
STUDY_CASES ITALY Illumina Global Screening Array (GSA) 140
STUDY_CONTROLS ITALY Illumina Global Screening Array (GSA) 891
STUDY_CONTROLS ITALY Illumina Global Screening Array (GSA) 364
EXTERNAL_CONTROLS SPAIN Illumina Human610-Quad 1471
EXTERNAL_CONTROLS SPAIN Illumina HumanCNV370k 347
EXTERNAL_CONTROLS SPAIN Illumina HumanCore 1242
EXTERNAL_CONTROLS SPAIN Illumina Infinium Multi-Ethnic Global Array 4976
EXTERNAL_CONTROLS ITALY Illumina Hap550k 946
EXTERNAL_CONTROLS ITALY Affymetrix 6.0 3327
STUDY_CASES SPAIN Illumina Global Screening Array (GSA) 301
STUDY_CASES SPAIN Illumina Global Screening Array (GSA) 45
STUDY_CASES SPAIN Illumina Global Screening Array (GSA) 201
STUDY_CASES SPAIN Illumina Global Screening Array (GSA) 228
STUDY_CONTROLS SPAIN Illumina Global Screening Array (GSA) 950
STUDY_CASES ITALY Illumina Global Screening Array (GSA) 503
STUDY_CASES ITALY Illumina Global Screening Array (GSA) 192
STUDY_CASES ITALY Illumina Global Screening Array (GSA) 140
STUDY_CONTROLS ITALY Illumina Global Screening Array (GSA) 891
STUDY_CONTROLS ITALY Illumina Global Screening Array (GSA) 364
EXTERNAL_CONTROLS SPAIN Illumina Human610-Quad 1471
EXTERNAL_CONTROLS SPAIN Illumina HumanCNV370k 347
EXTERNAL_CONTROLS SPAIN Illumina HumanCore 1242
EXTERNAL_CONTROLS SPAIN Illumina Infinium Multi-Ethnic Global Array 4976
EXTERNAL_CONTROLS ITALY Illumina Hap550k 946
EXTERNAL_CONTROLS ITALY Affymetrix 6.0 3327

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 Table S3
al and study independent TOPMed-imputed Spanish and Italian population-based GWAS control data sets from different genot

BATCH CHR POS

Cases, Donostia University Hospital, San Sebastian chr3 45834967
Cases, Hospital Clínic and IDIBAPS, Barcelona chr3 45834967
Cases, Hospital Universitario Ramón y Cajal, Madrid chr3 45834967
Cases, Hospital Universitario Vall d'Hebron, Barcelona chr3 45834967
Controls, Spain chr3 45834967
Cases, Fondazione IRCCS Cá Granda Ospedale Maggiore Policlinico, Milan chr3 45834967
Cases, UNIMIB School of Medicine, San Gerardo Hospital, Monza chr3 45834967
Cases, Humanitas Clinical and Research Center, IRCCS, Milan chr3 45834967
Controls, Italy 1 chr3 45834967
Controls, Italy 2 chr3 45834967
External Spanish controls 1 chr3 45834967
External Spanish controls 2 chr3 45834967
External Spanish controls 3 chr3 45834967
External Spanish controls 4 chr3 45834967
External Italian controls 1 chr3 45834967
External Italian controls 2 chr3 45834967
Cases, Donostia University Hospital, San Sebastian chr9 133263862
Cases, Hospital Clínic and IDIBAPS, Barcelona chr9 133263862
Cases, Hospital Universitario Ramón y Cajal, Madrid chr9 133263862
Cases, Hospital Universitario Vall d'Hebron, Barcelona chr9 133263862
Controls, Spain chr9 133263862
Cases, Fondazione IRCCS Cá Granda Ospedale Maggiore Policlinico, Milan chr9 133263862
Cases, UNIMIB School of Medicine, San Gerardo Hospital, Monza chr9 133263862
Cases, Humanitas Clinical and Research Center, IRCCS, Milan chr9 133263862
Controls, Italy 1 chr9 133263862
Controls, Italy 2 chr9 133263862
External Spanish controls 1 chr9 133263862
External Spanish controls 2 chr9 133263862
External Spanish controls 3 chr9 133263862
External Spanish controls 4 chr9 133263862
External Italian controls 1 chr9 133263862
External Italian controls 2 chr9 133263862

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 Table S3
ntrol data sets from different genotyping platforms.

SNP A1 A2 A1F A2F GENO_HOM_A1 GENO_HETGENO_HOM_A2

chr3:45834967:G:GA GA G 0.0714286 0.928571 0.00664452 0.129568 0.863787
chr3:45834967:G:GA GA G 0.122222 0.877778 0.0222222 0.2 0.777778
chr3:45834967:G:GA GA G 0.10199 0.89801 0.0149254 0.174129 0.810945
chr3:45834967:G:GA GA G 0.111842 0.888158 0.00877193 0.20614 0.785088
chr3:45834967:G:GA GA G 0.0505263 0.949474 0.00315789 0.0947368 0.902105
chr3:45834967:G:GA GA G 0.140159 0.859841 0.00994036 0.260437 0.729622
chr3:45834967:G:GA GA G 0.148438 0.851562 0.0208333 0.255208 0.723958
chr3:45834967:G:GA GA G 0.142857 0.857143 0.0142857 0.257143 0.728571
chr3:45834967:G:GA GA G 0.0920314 0.907969 0.00897868 0.166105 0.824916
chr3:45834967:G:GA GA G 0.092033 0.907967 0.021978 0.14011 0.837912
chr3:45834967:G:GA GA G 0.0611829 0.938817 0.00203943 0.118287 0.879674
chr3:45834967:G:GA GA G 0.0590778 0.940922 0.00864553 0.100865 0.89049
chr3:45834967:G:GA GA G 0.0603865 0.939614 0.00322061 0.114332 0.882448
chr3:45834967:G:GA GA G 0.0560691 0.943931 0.00241158 0.107315 0.890273
chr3:45834967:G:GA GA G 0.0924947 0.907505 0.00634249 0.172304 0.821353
chr3:45834967:G:GA GA G 0.100691 0.899309 0.0102194 0.180944 0.808837
chr9:133263862:A:C A C 0.408638 0.591362 0.182724 0.451827 0.365449
chr9:133263862:A:C A C 0.455556 0.544444 0.2 0.511111 0.288889
chr9:133263862:A:C A C 0.435323 0.564677 0.199005 0.472637 0.328358
chr9:133263862:A:C A C 0.416667 0.583333 0.153509 0.526316 0.320175
chr9:133263862:A:C A C 0.348421 0.651579 0.127368 0.442105 0.430526
chr9:133263862:A:C A C 0.421471 0.578529 0.178926 0.485089 0.335984
chr9:133263862:A:C A C 0.411458 0.588542 0.15625 0.510417 0.333333
chr9:133263862:A:C A C 0.442857 0.557143 0.164286 0.557143 0.278571
chr9:133263862:A:C A C 0.35073 0.64927 0.114478 0.472503 0.413019
chr9:133263862:A:C A C 0.354396 0.645604 0.145604 0.417582 0.436813
chr9:133263862:A:C A C 0.39191 0.60809 0.14208 0.49966 0.35826
chr9:133263862:A:C A C 0.371758 0.628242 0.149856 0.443804 0.40634
chr9:133263862:A:C A C 0.391304 0.608696 0.152979 0.476651 0.37037
chr9:133263862:A:C A C 0.362339 0.637661 0.133641 0.457395 0.408963
chr9:133263862:A:C A C 0.366279 0.633721 0.131078 0.470402 0.39852
chr9:133263862:A:C A C 0.392095 0.607905 0.151187 0.481815 0.366997

Page 3
 Table S3

IMP_STATUS IMP_R2
imputed 0.95515
imputed 0.95515
imputed 0.95515
imputed 0.95515
imputed 0.95515
imputed 0.94188
imputed 0.94188
imputed 0.94188
imputed 0.94188
imputed 0.94188
imputed 0.98792
imputed 0.98691
imputed 0.90049
imputed 0.97815
imputed 0.97727
imputed 0.98932
genotyped 1
genotyped 1
genotyped 1
genotyped 1
genotyped 1
genotyped 0.99974
genotyped 0.99974
genotyped 0.99974
genotyped 0.99974
genotyped 0.99974
genotyped 0.99991
imputed 0.93168
imputed 0.90248
genotyped 0.99999
genotyped 0.99737
imputed 0.96717

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