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Table 1 Top GWAS hits

From: Exploration of haplotype research consortium imputation for genome-wide association studies in 20,032 Generation Scotland participants

Baseline characteristic N dbSNP ID Minor allele frequency p value Gene Imputation quality Gene association reported previously? Region significant in genotyped data?
Cardiometabolic
 Diastolic blood pressure 19,546 rs142892876 0.0010 4.97E-08 CNTN6 0.75 No No
  rs528908640 0.0005 1.93E-08 OPA1 0.80 No No
  rs568998724 0.0007 2.91E-08 - 0.78 No No
  rs187680191 0.0006 2.94E-09 NRG4 0.51 No No
 Systolic blood pressure 19,547 None    None    
 Pulse pressure 19,546 None    None    
 Heart rate 19,920 rs9970334 0.4474 4.38E-08 ICMT 0.90 Yes No
  rs755291044 0.0017 1.80E-08 - 0.90 No No
  rs145669495 0.0022 2.01E-08 CSMD1 0.90 No No
  rs142916219 0.0037 2.21E-08 ASPH 0.85 No No
  rs365990 0.3637 4.04E-10 MYH6 0.99 Yes GWS
  rs148397504 0.0008 3.21E-09 - 0.45 No No
Biochemistry
 Serum creatinine 16,347 rs548873184 0.0010 1.47E-08 LINC00626 0.96 No No
  rs573421908 0.0027 1.35E-08 SLC35F3 0.80 Yes No
  rs62412107 0.0660 1.87E-08 - 0.79 No No
  rs3812036 0.2301 1.13E-10 SLC34A1 0.96 Yes GWS
 Fasting plasma glucose (with diabetics) 16,174 rs560887 0.2907 6.02E-68 G6PC2 1.00 Yes GWS
  rs9873618 0.2871 9.83E-12 SLC2A2 0.99 Yes GWS
  rs917793 0.1831 2.51E-24 YKT6 0.98 Yes GWS
  rs13266634 0.3153 3.66E-11 SLC30A8 1.00 Yes GWS
  rs533883198 0.0027 3.86E-08 - 0.84 No No
  rs7981781 0.2337 1.40E-08 PDX1 0.98 Yes GWS
  rs370189685 0.0014 7.32E-09 WDR4 0.63 No No
 Fasting plasma glucose (diabetics removed) 15,226 rs79687284 0.0364 1.87E-08 - 0.78 Yes GWS
  rs780095 0.4267 8.20E-09 GCKR 1.00 Yes GWS
  rs560887 0.2907 2.09E-75 G6PC2 1.00 Yes GWS
  rs8192675 0.2839 8.41E-11 SLC2A2 1.00 Yes GWS
  rs917793 0.1831 1.46E-28 YKT6 0.98 Yes GWS
  rs11558471 0.3227 4.63E-13 SLC30A8 1.00 Yes GWS
  rs143399767 0.0108 1.42E-08 Y_RNA 0.89 No No
  rs7981781 0.2337 5.01E-10 PDX1 0.98 Yes GWS
  rs370189685 0.0014 2.75E-08 WDR4 0.63 No Suggestive
 HDL cholesterol 19,223 rs149963466 0.0016 3.18E-08 - 0.76 No No
  rs76183280 0.0048 4.14E-08 AC016735.2 0.78 No No
  rs4841132 0.0925 1.08E-08 RP11-115 J16.1 1.00 Yes Suggestive
  rs15285 0.2675 1.16E-18 LPL 1.00 Yes GWS
  rs2740488 0.2745 2.53E-08 ABCA1 1.00 Yes GWS
  rs138326449 0.0032 2.92E-20 APOC3 0.85 Yes No
  rs114529226 0.0038 6.98E-09 IGHVII-33-1 0.64 No No
  rs261290 0.3442 2.78E-25 ALDH1A2 1.00 Yes GWS
  rs3764261 0.3261 1.40E-113 CETP 1.00 Yes GWS
  rs143264468 0.0010 1.99E-09 LRRC29 0.81 Yes Suggestive
  rs72836561 0.0294 1.55E-11 CD300LG 0.87 Yes No
  rs149615216 0.0119 3.20E-09 LIPG 0.97 Yes Suggestive
  rs116843064 0.0230 5.57E-10 ANGPTL4 0.84 Yes No
  rs7412 0.0779 5.95E-14 APOE 0.98 Yes GWS
  rs453755 0.2480 3.22E-08 LILRA3 0.92 Yes No
  rs435306 0.2547 2.87E-08 PLTP 1.00 Yes Suggestive
 Cholesterol 19,259 rs11591147 0.0169 1.83E-17 PCSK9 0.98 Yes GWS
  rs10889333 0.3601 2.12E-10 DOCK7 1.00 Yes GWS
  rs12740374 0.2288 8.19E-22 CELSR2 1.00 Yes GWS
  rs672889 0.1356 3.77E-16 - 1.00 Yes GWS
  rs75331444 0.0720 1.87E-11 ABCG8 0.99 Yes GWS
  rs12916 0.3970 6.35E-11 HMGCR 0.99 Yes GWS
  rs74617384 0.0838 3.02E-09 LPA 0.93 Yes No
  rs4841133 0.0929 2.51E-09 RP11-115 J16.1 1.00 Yes Suggestive
  rs2000999 0.1776 7.01E-09 HPR 0.99 Yes Suggestive
  rs10412048 0.1086 5.00E-25 - 0.98 Yes GWS
  rs7412 0.0779 5.22E-94 APOE 0.98 Yes GWS
 Urea 19,293 rs760077 0.4247 6.24E-09 MTX1 0.98 Yes Suggestive
  rs16862780 0.1574 3.03E-10 RP11-132 N15.3 1.00 Yes GWS
  rs112647987 0.0680 3.07E-08 - 0.99 No No
  rs6950388 0.1872 1.57E-08 UNCX 0.95 Yes GWS
  rs10224210 0.2799 5.71E-09 PRKAG2 0.92 Yes Suggestive
Anthropometric
 Body mass index 19900 rs73139123 0.1830 1.34E-09 - 0.96 Yes GWS
  rs10498218 0.0012 3.98E-08 COL4A4 0.84 Yes No
  rs149913955 0.0059 2.18E-08 RP11-624 L4.1 0.74 No No
  rs571835655 0.0011 6.61E-09 - 0.82 No No
  rs55872725 0.3951 5.71E-21 FTO 1.00 Yes GWS
 Height 19,965 rs146949893 0.0031 4.49E-08 RP1-35C21.2 0.72 No No
  rs558671668 0.0062 2.53E-08 RP11-317P15.6 0.80 No No
  rs6765866 0.0007 2.05E-08 CMTM8 0.59 No No
  rs1991431 0.4338 5.25E-13 ZBTB38 1.00 Yes GWS
  rs35362908 0.1006 7.04E-09 LCORL 0.73 Yes No
  rs552283803 0.0016 3.99E-08 ARHGAP24 0.79 No No
  rs755546258 0.0007 2.58E-08 DAP 0.72 No No
  rs72742734 0.0537 3.61E-08 NPR3 1.00 Yes Suggestive
  rs554379257 0.0006 4.83E-08 CTD-2023 N9.1 0.44 No No
  rs7766641 0.2551 3.32E-13 HIST1H2BE 1.00 Yes GWS
  rs57026767 0.1550 4.50E-11 C6orf1 1.00 Yes GWS
  rs566773279 0.0005 1.17E-08 - 0.69 No No
  rs1490384 0.4851 7.09E-10 - 1.00 Yes GWS
  rs7753012 0.3072 7.60E-14 GPR126 0.99 Yes GWS
  rs184469050 0.0088 1.58E-08 - 0.89 No No
  rs144225905 0.0010 2.13E-09 - 0.46 No No
  rs7952436 0.0896 1.91E-12 KDM2A 0.88 Yes No
  rs634552 0.1365 2.30E-08 SERPINH1 0.98 Yes GWS
  rs76895963 0.0285 3.43E-08 CCND2 0.78 Yes [48, 49] No
  rs770307181 0.0005 1.09E-08 - 0.50 No No
  rs139770682 0.0005 4.55E-08 - 0.72 No No
  rs11614062 0.1943 2.09E-08 SOCS2-AS1 0.99 Yes GWS
  rs75061684 0.0006 5.33E-10 - 0.49 No No
  rs16942323 0.0344 1.09E-11 ACAN 0.93 Yes No
  rs8096254 0.2598 4.32E-12 CABLES1 1.00 Yes GWS
  rs6060402 0.3585 2.80E-13 - 0.98 Yes GWS
 Waist-to-hip ratio 19,695 rs72959041 0.0566 2.54E-14 RSPO3 0.90 Yes Suggestive
  rs149924309 0.0023 3.70E-08 - 0.81 No No
  rs187209742 0.0023 4.91E-08 SERPINA10 0.70 No No
  rs751156121 0.0006 1.29E-08 - 0.78 No No
 Body fat 19,480 rs10921288 0.0235 1.04E-08 - 0.99 No GWS
  rs142101835 0.0022 3.25E-08 IRS1 0.69 Yes No
  rs560546550 0.0007 3.17E-09 WDR41 0.89 No No
  rs571835655 0.0011 2.03E-08 - 0.82 No No
  rs55872725 0.3951 5.55E-16 FTO 1.00 Yes GWS
  rs141793746 0.0030 3.31E-08 DYM 0.86 No No
NHS EHR linkage
 Serum urate 2077 rs6449213 0.1652 1.93E-17 SLC2A9 1.00 Yes GWS
  rs75869162 0.0054 1.57E-08 FAM134B 0.80 No No
  rs141208451 0.0053 3.13E-09 RP11-430H10.4 0.86 No No
  rs187171029 0.0060 1.84E-08 ZNF160 0.91 No No
  1. Summary of the baseline characteristics of the GS:SFHS sub-cohort of 20,032 analysed by GWAS, with genome-wide significant markers from the imputed GWAS listed. We indicate known associations in published research or present in the NHGRI GWAS Catalog within 100 kb of the sentinal SNP reported here. The column called ‘Region significant in genotyped data?’ indicates whether any SNPs within 500 kb of the reported SNP reach genome-wide significance (GWS, p < 5*10–8) or suggestive significance (Suggestive, p < 10–5) in the genotyped data