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 | |
PCSK9 | rs11591147 | LDL cholesterol | 6602 | 0.038 | –0.406 (0.053) | WGS + imputation | SardiNIA | Sardinian | |
PCSK9 | rs11591147 | Triglycerides | 6602 | 0.038 | –0.390 (0.053) | WGS + imputation | SardiNIA | Sardinian | |
EN1 | rs55983207 | BMD | 45,436 | 0.05 | 0.12 | WGS + WES + imputation | UK10K and others | European | |
EN1 | rs11692564 | BMD | 40,516 | 0.016 | 0.22 | WGS + WES + imputation | UK10K and others | European | |
EN1 | rs188303909 | BMD | 40,453 | 0.03 | 0.16 | WGS + WES + imputation | UK10K and others | European | |
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 | |
ADIPOQ | rs17366653 | Adiponectin | 3621 | 0.01 | –1.029 (0.150) | WGS | UK10K | British | |
GHR | rs121909358 | Height | 6307 | 0.0087 (<0.0001) | –0.64 | WGS + imputation | SardiNIA | Sardinian | |
TMEM161B | rs774396010 | HDL cholesterol | 3621 | 0.001 | –1.887 (0.378) | WGS | UK10K | British | |
PAM | rs35658696 | Type 2 diabetes | 278,254 | 0.0498 | 1.22 | WGS + imputation | deCODE | Icelandic | |
GLP1R | rs10305492 | Fasting glucose | 60,564 | 0.01 | –0.09 (0.013) | GWAS + WES | CHARGE | African and European | |
TREM2 | rs75932628 | Alzheimer’s disease | 110,050 | 0.0063 | 2.26 | WGS + imputation | deCODE | Icelandic | |
CCND3 | rs112233623 | MCV | 107,686 | 0.011 | 0.739 (0.05) | WGS + imputation | UK10K and others | European | |
WNT16 | rs148771817 | BMD | 10,387 | 0.012 | 0.46 | WGS + WES + imputation | UK10K and others | European | |
ABCA1 | rs3824477 | HDL cholesterol | 56,598 | 0.026 | 0.123 (0.016) | WGS + imputation | UK10K and others | European | |
FNBP1 | rs528899443 | FEV1/FVC | 3621 | 0.004 | 1.078 (0.204) | WGS | UK10K | British | |
GFI1B | rs150813342 | PLT | 114,753 | 0.004 | –0.406 (0.026) | WGS + imputation | UK10K and others | European | |
GFI1B | rs150813342 | PLT | 13,744 | 0.008 | –0.402 (0.07) | WES | Six cohort studies | European and African American | |
ANK3 | rs141471070 | FEV1/FVC | 3621 | 0.006 | 0.739 (0.164) | WGS | UK10K | British | |
KCNQ1 | rs150199504 | Height | 6307 | 0.07 (<0.01) | –0.31 | WGS + imputation | SardiNIA | Sardinian | |
HBB | rs11549407 | Cholesterol, total | 6602 | 0.048 | –0.490 (0.05) | WGS + imputation | SardiNIA | Sardinian | |
HBB | rs11549407 | LDL cholesterol | 6602 | 0.048 | –0.473 (0.051) | WGS + imputation | SardiNIA | Sardinian | |
SMCO4 | rs111902751 | FVC | 3621 | 0.014 | –0.505 (0.103) | WGS | UK10K | British | |
APOA5 | rs778114184 | Triglycerides | 6602 | 0.025 | –0.450 (0.064) | WGS + imputation | SardiNIA | Sardinian | |
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 | |
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 | |
VWF | rs149424724 | VWF antigen | 4468 | 0.008 | –40.3 (10.0) | WES | ESP of NHLBI | European or African | |
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 | |
NPRL3 | rs117747069 | MCH | 120,851 | 0.037 | –0.176 (0.024) | WGS + imputation | UK10K and others | European | |
CDH13 | rs12051272 | Adiponectin | 3621 | 0.009 | –1.074 (0.156) | WGS | UK10K | British | |
APOH | rs1801689 | PLT | 13,5097 | 0.033 | 0.104 (0.012) | WGS + imputation | UK10K and others | European | |
ABCA6 | rs77542162 | Cholesterol, total | 35,000 | 0.034 | 0.14 | WGS + imputation | GoNL | Dutch | |
ABCA6 | rs77542162 | LDL cholesterol | 35,000 | 0.034 | 0.135 | WGS + imputation | GoNL | Dutch | |
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 | |
LDLR | rs72658867 | LDL cholesterol | 3621 | 0.012 | –0.584 (0.112) | WGS | UK10K | British | |
APOE | rs7412 | LDL cholesterol | 6602 | 0.036 | –0.645 (0.053) | WGS + imputation | SardiNIA | Sardinian | |
APOE | rs7412 | Triglycerides | 6602 | 0.036 | –0.544 (0.053) | WGS + imputation | SardiNIA | Sardinian | |
APP | rs63750847 | Alzheimer’s disease | 71,743 | 0.00467 | 0.189 | WGS + imputation | deCODE | Icelandic | |
LGR4 | hg18_chr11:27369242_A | BMD | 95,085 | 0.00174 | –0.75 (0.16) | WGS + imputation | deCODE | Icelandic | |
PDX1 | hg18_chr13:27396636delT | Type 2 diabetes | 278,254 | 0.00198 | 2.47 | WGS + imputation | deCODE | Icelandic |