Table 1.
Top GWAS hits
| 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 | ||
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