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Table 3 Rare variants (AF <5%) discovered in WGS, WES and imputed studies and found to be associated with various traits

From: The impact of rare and low-frequency genetic variants in common disease

Gene Variant ID Trait/disease Samples AF (cases/controls) Beta/OR (SE)/(CI) Type Study Population Reference
PCSK9 rs11591147 LDL cholesterol 3621 0.022 –0.470 (0.085) WGS UK10K British http://www.ncbi.nlm.nih.gov/pubmed/26367797
PCSK9 rs11591147 LDL cholesterol 6602 0.038 –0.406 (0.053) WGS + imputation SardiNIA Sardinian http://www.ncbi.nlm.nih.gov/pubmed/26366554
PCSK9 rs11591147 Triglycerides 6602 0.038 –0.390 (0.053) WGS + imputation SardiNIA Sardinian http://www.ncbi.nlm.nih.gov/pubmed/26366554
EN1 rs55983207 BMD 45,436 0.05 0.12 WGS + WES + imputation UK10K and others European http://www.ncbi.nlm.nih.gov/pubmed/26367794
EN1 rs11692564 BMD 40,516 0.016 0.22 WGS + WES + imputation UK10K and others European http://www.ncbi.nlm.nih.gov/pubmed/26367794
EN1 rs188303909 BMD 40,453 0.03 0.16 WGS + WES + imputation UK10K and others European http://www.ncbi.nlm.nih.gov/pubmed/26367794
CCDC36 rs202238847 Height 51,309 0.021 0.1091 (0.0233) WGS + imputation UK10K British Tachmazidou et al. (in press)
ADIPOQ rs74577862 Adiponectin 3621 0.026 –0.915 (0.091) WGS UK10K British http://www.ncbi.nlm.nih.gov/pubmed/26367797
ADIPOQ rs17366653 Adiponectin 3621 0.01 –1.029 (0.150) WGS UK10K British http://www.ncbi.nlm.nih.gov/pubmed/26367797
GHR rs121909358 Height 6307 0.0087 (<0.0001) –0.64 WGS + imputation SardiNIA Sardinian http://www.ncbi.nlm.nih.gov/pubmed/26366551
TMEM161B rs774396010 HDL cholesterol 3621 0.001 –1.887 (0.378) WGS UK10K British http://www.ncbi.nlm.nih.gov/pubmed/26367797
PAM rs35658696 Type 2 diabetes 278,254 0.0498 1.22 WGS + imputation deCODE Icelandic http://www.ncbi.nlm.nih.gov/pubmed/24464100
GLP1R rs10305492 Fasting glucose 60,564 0.01 –0.09 (0.013) GWAS + WES CHARGE African and European http://www.ncbi.nlm.nih.gov/pubmed/25631608
TREM2 rs75932628 Alzheimer’s disease 110,050 0.0063 2.26 WGS + imputation deCODE Icelandic http://www.ncbi.nlm.nih.gov/pubmed/23150908
CCND3 rs112233623 MCV 107,686 0.011 0.739 (0.05) WGS + imputation UK10K and others European https://www.ncbi.nlm.nih.gov/pubmed/27668658
WNT16 rs148771817 BMD 10,387 0.012 0.46 WGS + WES + imputation UK10K and others European http://www.ncbi.nlm.nih.gov/pubmed/26367794
ABCA1 rs3824477 HDL cholesterol 56,598 0.026 0.123 (0.016) WGS + imputation UK10K and others European https://www.ncbi.nlm.nih.gov/pubmed/27668658
FNBP1 rs528899443 FEV1/FVC 3621 0.004 1.078 (0.204) WGS UK10K British http://www.ncbi.nlm.nih.gov/pubmed/26367797
GFI1B rs150813342 PLT 114,753 0.004 –0.406 (0.026) WGS + imputation UK10K and others European https://www.ncbi.nlm.nih.gov/pubmed/27668658
GFI1B rs150813342 PLT 13,744 0.008 –0.402 (0.07) WES Six cohort studies European and African American http://www.ncbi.nlm.nih.gov/pubmed/27486782
ANK3 rs141471070 FEV1/FVC 3621 0.006 0.739 (0.164) WGS UK10K British http://www.ncbi.nlm.nih.gov/pubmed/26367797
KCNQ1 rs150199504 Height 6307 0.07 (<0.01) –0.31 WGS + imputation SardiNIA Sardinian http://www.ncbi.nlm.nih.gov/pubmed/26366551
HBB rs11549407 Cholesterol, total 6602 0.048 –0.490 (0.05) WGS + imputation SardiNIA Sardinian http://www.ncbi.nlm.nih.gov/pubmed/26366554
HBB rs11549407 LDL cholesterol 6602 0.048 –0.473 (0.051) WGS + imputation SardiNIA Sardinian http://www.ncbi.nlm.nih.gov/pubmed/26366554
SMCO4 rs111902751 FVC 3621 0.014 –0.505 (0.103) WGS UK10K British http://www.ncbi.nlm.nih.gov/pubmed/26367797
APOA5 rs778114184 Triglycerides 6602 0.025 –0.450 (0.064) WGS + imputation SardiNIA Sardinian http://www.ncbi.nlm.nih.gov/pubmed/26366554
APOC3 rs138326449 Triglycerides 3621 0.003 –1.425 (0.265) WGS UK10K British dx.doi.org/10.1038/ncomms5871
APOC3 rs138326449 Triglycerides 3734 0.001 NA WES ESP of NHLBI European or African http://www.ncbi.nlm.nih.gov/pubmed/24941081
APOC3 rs138326449 VLDL 3621 0.003 –1.426 (0.265) WGS UK10K British dx.doi.org/10.1038/ncomms5871
CCND2 rs76895963 Type 2 diabetes 278,254 0.0147 0.53 WGS + imputation deCODE Icelandic http://www.ncbi.nlm.nih.gov/pubmed/24464100
VWF rs61750625 VWF antigen 4468 0.00763 –39.6 (9.71) WES ESP of NHLBI European or African http://www.ncbi.nlm.nih.gov/pubmed/23690449
VWF rs149424724 VWF antigen 4468 0.008 –40.3 (10.0) WES ESP of NHLBI European or African http://www.ncbi.nlm.nih.gov/pubmed/23690449
VWF rs150077670 VWF antigen 4468 0.0044 –34.5 (12.7) WES ESP of NHLBI European or African http://www.ncbi.nlm.nih.gov/pubmed/23690449
MBIP rs116909374 TSH (thyrotropin) 15,037 0.043 –0.208 (0.032) WGS + imputation UK10K British DOI: 10.1038/ncomms6681
SERPINA1 rs28929474 Height 49,889 0.019 0.1346 (0.0253) WGS + imputation UK10K British Tachmazidou et al. (in press)
TP53BP1 rs575505283 PLT 121,793 0.014 –0.162 (0.019) WGS + imputation UK10K and others European https://www.ncbi.nlm.nih.gov/pubmed/27668658
NPRL3 rs117747069 MCH 120,851 0.037 –0.176 (0.024) WGS + imputation UK10K and others European https://www.ncbi.nlm.nih.gov/pubmed/27668658
CDH13 rs12051272 Adiponectin 3621 0.009 –1.074 (0.156) WGS UK10K British http://www.ncbi.nlm.nih.gov/pubmed/26367797
APOH rs1801689 PLT 13,5097 0.033 0.104 (0.012) WGS + imputation UK10K and others European https://www.ncbi.nlm.nih.gov/pubmed/27668658
ABCA6 rs77542162 Cholesterol, total 35,000 0.034 0.14 WGS + imputation GoNL Dutch http://www.ncbi.nlm.nih.gov/pubmed/25751400
ABCA6 rs77542162 LDL cholesterol 35,000 0.034 0.135 WGS + imputation GoNL Dutch http://www.ncbi.nlm.nih.gov/pubmed/25751400
B4GALT6 rs113107469 FT4 (free thyroxine) 13,649 0.032 0.223 (0.037) WGS + imputation UK10K British DOI: 10.1038/ncomms6681
C3 rs147859257 AMD 52,578 0.0055 3.13 (1.99–4.91) WGS + imputation deCODE Icelandic http://www.ncbi.nlm.nih.gov/pubmed/24036950
LDLR rs72658867 ApoB 3621 0.012 –0.538 (0.119) WGS UK10K British http://www.ncbi.nlm.nih.gov/pubmed/26367797
LDLR rs72658867 LDL cholesterol 3621 0.012 –0.584 (0.112) WGS UK10K British http://www.ncbi.nlm.nih.gov/pubmed/26367797
APOE rs7412 LDL cholesterol 6602 0.036 –0.645 (0.053) WGS + imputation SardiNIA Sardinian http://www.ncbi.nlm.nih.gov/pubmed/26366554
APOE rs7412 Triglycerides 6602 0.036 –0.544 (0.053) WGS + imputation SardiNIA Sardinian http://www.ncbi.nlm.nih.gov/pubmed/26366554
APP rs63750847 Alzheimer’s disease 71,743 0.00467 0.189 WGS + imputation deCODE Icelandic http://www.ncbi.nlm.nih.gov/pubmed/22801501
LGR4 hg18_chr11:27369242_A BMD 95,085 0.00174 –0.75 (0.16) WGS + imputation deCODE Icelandic http://www.ncbi.nlm.nih.gov/pubmed/23644456
PDX1 hg18_chr13:27396636delT Type 2 diabetes 278,254 0.00198 2.47 WGS + imputation deCODE Icelandic http://www.ncbi.nlm.nih.gov/pubmed/24464100
  1. AF allele frequency, AMD age-related macular degeneration, BMD, bone mineral density, CI confidence interval, ESP Exome Sequencing Project, FEV forced expiratory volume, FVC forced vital capacity, HDL high-density lipoprotein, LDL low-density lipoprotein, MCH mean cell haemoglobin, MCV mean cell volume, NA not applicable, NHLBI National Heart, Lung, and Blood Institute, OR odds ratio, PLT platelet count, SE standard error, WES whole-exome sequencing, WGS whole-genome sequencing, VLDL very low-density lipoprotein, VWF Von Willebrand factor