Spreadsheet: bcdfef77-acd2-40fe-aa01-1aa3b99159f1
Sheet: Sheet1

Table S6: Lead markers and proxies used in stage 2 replication.  The upper-portion of the table shows descriptives for the lead marker at each locus, and the lower portion shows which marker was analyzed in each study - the lead SNP ("lead"), a proxy, or  if no data was available at the locus. | Unnamed: 1 | Unnamed: 2 | Unnamed: 3 | Unnamed: 4 | Unnamed: 5 | Unnamed: 6 | Unnamed: 7 | Unnamed: 8 | Unnamed: 9 | Unnamed: 10 | Unnamed: 11 | Unnamed: 12 | Unnamed: 13 | Unnamed: 14 | Unnamed: 15 | Unnamed: 16 | Unnamed: 17 | Unnamed: 18 | Unnamed: 19 | Unnamed: 20 | Unnamed: 21 | Unnamed: 22 | Unnamed: 23 | Unnamed: 24 | Unnamed: 25 | Unnamed: 26
Gene/Locus | near HCRTR2 (6p11-q11) | near ECHDC3 (10p14) | near ATP6V1C2 (2p25.1) | DCTD (4q35.1) | [NAME] (6p25.3) | PCSK2 (20p11.2) | [NAME] (10p15.3) | PDGFRL (8p22-p21.3) | TCF12 (15q21) | near LYPLAL1 (1q41) | [NAME] (6p25.3) | CYP2A6 (19q13.2) | near TFAP2B (6p12) | [NAME] (8p23.3) | [NAME] (11q24.2) | TBCE (1q42.3) | IPO8 (12p11.21) | near BARHL2 (1p22.2) | near [NAME] (5q33.3) | MKL2 (16p13.3) | near MSRA (8p23.1) | near HMGA2 (12q15) | [NAME] (14p13) | PSME4 (2p16.1) | TFAP2B (6p12) | [NAME] (3p12.2)
Chromosome | 6 | 10 | 2 | 4 | 6 | 20 | 10 | 8 | 15 | 1 | 6 | 8 | 6 | 8 | 11 | 1 | 12 | 1 | 5 | 16 | 8 | 12 | 14 | 2 | 6 | 3
Lead SNP | rs11970116 | rs12414558 | rs12993133 | rs13116494 | rs1328884 | rs16998899 | rs17321467 | rs2245667 | rs2414500 | rs2605100 | rs3761987 | rs406796 | rs4715215 | rs4737325 | rs608501 | rs6429082 | rs6487924 | rs6699397 | rs6892723 | rs7194591 | rs7826222 | rs7970350 | rs8014476 | rs805412 | rs987237 | rs7620339
Position (Build 35) | 55108104 | 11766559 | 10796800 | 184200851 | 8535417 | 17209305 | 7078267 | 17505605 | 55383642 | 216032619 | 14583506 | 68660395 | 51068275 | 72780191 | 124796855 | 231926170 | 30676485 | 90924237 | 157099895 | 14171131 | 9897490 | 64646431 | 41662791 | 54032471 | 50911009 | 85945340
Minor allele | A | A | C | A | A | C | T | C | G | A | T | G | C | C | A | T | C | G | G | C | G | T | G | A | G | A
Major allele | T | G | T | C | C | A | C | G | A | G | A | A | T | T | G | C | T | A | C | G | C | C | A | G | A | G
MAF min | 0.2362288136 | 0.0430847212 | 0.1098591549 | 0.2906403941 | 0.0718181818 | 0.0349576271 | 0.0994052676 | 0.2947548461 | 0.277994 | 0.2479289941 | 0.3454157783 | 0.2480270575 | 0.2821888412 | 0.1272513045 | 0.347133758 | 0.4065143928 | 0.2153748412 | 0.2796157951 | 0.277738 | 0.0152693 | 0.1206 | 0.3781914894 | 0.0316666667 | 0.3924 | 0.1305418719 | 0.185
MAF max | 0.3531659389 | 0.1798715203 | 0.321833 | 0.5044856459 | 0.156587473 | 0.0835526316 | 0.2076473712 | 0.4532902468 | 0.5102591793 | 0.367113 | 0.577048 | 0.3889209463 | 0.395528 | 0.2157622739 | 0.6 | 0.4965986395 | 0.280706 | 0.5979064039 | 0.3861283644 | 0.0433280819 | 0.2085755814 | 0.5150669643 | 0.097398 | 0.4894067797 | 0.240752 | 0.201
Stage 1: Genome-wide association studies
Cohorte Lausannoise (CoLaus) Study | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead
deCODE genetics discovery samples | lead | rs17461318 | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead
Stage 2a: Replication studies in-silico
[NAME] study (ERF) | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead |  | lead | lead | lead | lead
[NAME] (ERGO) | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead
Fenland study | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead
Genetic Epidemiology of Metabolic Syndrome (GEMS) Cases | lead | lead | lead | lead | lead | lead | lead |  | lead | lead | lead | lead |  | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead
Genetic Epidemiology of Metabolic Syndrome (GEMS) Controls | lead | lead | lead | lead | lead | lead | lead | lead |  | lead | lead | lead |  | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead
London Life Sciences Population Study - Northern Europeans (LOLIPOP-NE) | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead
Precocious Coronary Artery Disease (ProCARDIS) | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead |  | lead | lead | lead | lead | lead
Twins UK replication samples | lead |  |  | lead | rs330125 | lead | lead | lead | lead |  | lead | lead | lead |  | lead | lead | rs10843797 | lead | lead | lead | rs545854 |  | lead | lead | lead
Stage 2b: Replication studies bespoke genotyping
Prevalence, Prediction and Prevention of Diabetes in the Botnia study (BPPP) | rs12194068 |  | rs17364596 |  | lead | rs16998895 | lead | lead | rs2544129 | lead | lead | lead |  |  | lead | rs12405889 | rs10843797 | rs1526480 | lead | lead | rs545854 | lead | lead | rs698854 | lead
British 1958 [NAME] replication samples |  |  |  |  |  |  | rs11254929* |  |  | lead | lead | lead |  |  |  | lead |  | lead
British Women Health Study (BWHS) | lead |  |  |  |  | lead | lead |  |  | lead | lead |  |  |  |  | lead |  | lead |  |  |  | lead |  |  | lead
deCODE genetics replication samples | lead | rs17461318 | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead
National FINRISK study, 1997 | rs12194068 | lead | rs17364596 |  | lead | rs16998895 | lead | lead | rs2544129 | lead | lead | lead |  | lead | lead | rs12405889 | rs10843797 | rs1526480 | lead |  | rs545854 | lead | lead | rs698854 | lead
Finland-United States Investigation of NIDDM Genetics Stage 2 (FUSION S2) Cases | lead | rs17461318 |  | lead |  | lead | lead | lead | lead* | lead | lead | lead | lead | lead | lead |  | lead | lead | lead |  | lead | lead | rs7156383 | lead | lead
Finland-United States Investigation of NIDDM Genetics Stage 2 (FUSION S2) Controls | lead | rs17461318 |  | lead |  | lead | lead | lead | lead* | lead | lead | lead | lead | lead | lead |  | lead | lead | lead |  | lead | lead | rs7156383 | lead | lead
Hertfortshire Cohort Study | lead | lead | lead | lead | rs330125 | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | rs10843797 | lead | lead | lead | lead | lead | lead* | lead* | lead
KOoperative gesundheitsforschung in der Region Augsburg (KORA), [NAME] | lead |  |  |  | rs330125 |  | lead | lead |  | rs2605097 | lead | lead | lead |  | lead |  |  |  | lead |  |  | lead |  | lead | lead
Metabolic Syndrome in Men (METSIM) | lead | rs17461318 |  | lead |  | lead | lead |  |  | lead | lead | lead | lead | lead | lead |  | lead | lead | lead |  | lead | lead | rs7156383 | lead | lead
MRC [NAME] | lead | lead | lead | lead | rs330125 | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | rs10843797 | lead | lead | lead | rs545854 | lead | lead | lead | lead
Nurses Health Study (NHS) - Cases |  |  | lead | lead | lead | rs16998895 |  | lead | lead | lead |  | rs11997518 |  | lead | lead |  | lead | lead | rs1039322 | lead |  | lead | lead |  | lead
Nurses Health Study (NHS) - Controls |  |  | lead | lead | lead | rs16998895 |  | lead | lead | lead |  | rs11997518 |  | lead | lead |  | lead | lead | rs1039322 | lead |  | lead | lead |  | lead
UK Type 2 Diabetes Genetics Consortium collection replication set 1 Cases |  |  |  |  |  |  | rs11254929 |  |  | lead | lead | lead |  |  |  | lead |  | lead
UK Type 2 Diabetes Genetics Consortium collection replication set 1 Controls |  |  |  |  |  |  | rs11254929 |  |  | lead | lead | lead |  |  |  | lead |  | lead
UK Type 2 Diabetes Genetics Consortium collection replication set 3 Cases |  |  |  |  |  |  | rs11254929 |  |  | lead | lead | lead |  |  |  | lead |  | lead
UK Type 2 Diabetes Genetics Consortium collection replication set 3 Controls |  |  |  |  |  |  | rs11254929 |  |  | lead | lead | lead |  |  |  | lead |  | lead
UK Type 2 Diabetes Genetics Consortium collection replication set 4 Cases |  |  |  |  |  |  | rs11254929 |  |  | lead | lead | lead |  |  |  | lead |  | lead
UK Type 2 Diabetes Genetics Consortium collection replication set 4 Controls |  |  |  |  |  |  | rs11254929 |  |  | lead | lead | lead |  |  |  | lead |  | lead
[NAME] of Obesity (UGO) | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead | lead
The data here presents all attempted markers for follow-up, a few of which failed QC criteria and was subsequently not included in analysis