Table 3. CHARGE meta-analysis results, ordered by locus and trait, and HaemGen replication analysis.
| CHARGE | HaemGen | CHARGE + HaemGen | |||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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| Locus# | Trait | SNPID | Chr | PhysPos | min_all | MAF | Gene | % Var | Beta | s.e. | P | Beta | s.e. | P | Beta | s.e. | P |
| 2 | Hct | rs10168349 | 2 | 46208555 | C | 0.341667 | PRKCE | 0.16% | 0.201 | 0.0283 | 1.176E-12 | 0.1524 | 0.0471 | 0.001212 | 0.1875 | 0.0238 | 3.748E-15 |
| 6 | Hct | rs1800562 | 6 | 26201120 | A | 0.041667 | HFE | 0.09% | 0.3747 | 0.0608 | 7.204E-10 | 0.1167 | 0.1004 | 0.245 | 0.3073 | 0.0513 | 2.035E-09 |
| 9 | Hct | rs9483788 | 6 | 135477194 | C | 0.177966 | HBS1L/MYB | 0.13% | 0.2172 | 0.0328 | 3.551E-11 | 0.2147 | 0.0527 | 4.55E-05 | 0.2166 | 0.0274 | 2.811E-15 |
| 12 | Hct | rs7385804 | 7 | 100073906 | C | 0.377358 | TFR 2 | 0.17% | -0.1592 | 0.0286 | 2.745E-08 | -0.1269 | 0.0478 | 0.00799 | -0.151 | 0.0242 | 4.45E-10 |
| 13 | Hct | rs10224002 | 7 | 151045974 | G | 0.258333 | PRKAG2 | 0.22% | 0.1691 | 0.0299 | 1.492E-08 | 0.2727 | 0.0493 | 3.08E-08 | 0.1963 | 0.0252 | 6.045E-15 |
| 16 | Hct | rs16926246 | 10 | 70763398 | T | 0.110169 | HK1 | 0.13% | 0.337 | 0.0513 | 4.986E-11 | 0.3094 | 0.096 | 0.00127 | 0.3315 | 0.0445 | 9.636E-14 |
| 17 | Hct | rs11065987 | 12 | 110556807 | G | 0.341667 | SH 2B3/ATXN 2 | 0.15% | -0.1809 | 0.0288 | 3.343E-10 | -0.1438 | 0.0465 | 0.001983 | -0.171 | 0.0241 | 1.363E-12 |
| 22 | Hct | rs2413450 | 22 | 35800170 | T | 0.381818 | TMPRSS6 | 0.10% | -0.162 | 0.0279 | 6.333E-09 | -0.2082 | 0.0467 | 8.13E-06 | -0.1736 | 0.0236 | 1.846E-13 |
| 2 | Hgb | rs10495928 | 2 | 46206670 | G | 0.341667 | PRKCE | 0.10% | 0.011 | 0.011 | 5.926E-10 | 0.0537 | 0.0152 | 0.000414 | 0.0631 | 0.0088 | 7.052E-13 |
| 6 | Hgb | rs1800562 | 6 | 26201120 | A | 0.041667 | HFE | 0.17% | 0.0224 | 0.0224 | 3.592E-16 | 0.1167 | 0.0322 | 0.000295 | 0.1617 | 0.0182 | 5.737E-19 |
| 13 | Hgb | rs10224002 | 7 | 151045974 | G | 0.258333 | PRKAG2 | 0.14% | 0.011 | 0.011 | 4.605E-08 | 0.0964 | 0.0164 | 4.19E-09 | 0.0714 | 0.0091 | 3.025E-15 |
| 16 | Hgb | rs16926246 | 10 | 70763398 | T | 0.110169 | HK1 | 0.21% | 0.0192 | 0.0192 | 1.036E-09 | 0.0863 | 0.0329 | 0.008721 | 0.1099 | 0.0164 | 2.116E-11 |
| 17 | Hgb | rs11065987 | 12 | 111076069 | A | 0.333333 | TRAFD1 | 0.16% | 0.0107 | 0.0107 | 1.345E-10 | 0.0427 | 0.0151 | 0.004591 | 0.0585 | 0.0086 | 1.159E-11 |
| 21 | Hgb | rs6013509 | 20 | 50751758 | A | 0.183673 | TSHZ2 | 0.15% | -0.0699 | 0.0116 | 1.963E-09 | -0.0479 | 0.0206 | 0.01999 | -0.0646 | 0.01 | 1.054E-10 |
| 22 | Hgb | rs855791 | 22 | 35792882 | A | 0.391667 | TMPRSS6 | 0.20% | -0.0962 | 0.011 | 2.044E-18 | -0.0845 | 0.0157 | 7.97E-08 | -0.0923 | 0.0089 | 3.25E-25 |
| 4 | MCH | rs11915082 | 3 | 197293536 | A | 0.425 | TFRC | 0.24% | 0.0041 | 0.0007 | 4.888E-09 | 0.0035 | 0.0009 | 5.66E-05 | 0.0038 | 0.0005 | 7.729E-13 |
| 6 | MCH | rs1408272 | 6 | 25950930 | G | 0.033898 | SLC17A3 | 0.41% | -0.0134 | 0.0015 | 1.369E-18 | -0.0183 | 0.0019 | 2.37E-22 | -0.0153 | 0.0012 | 3.868E-39 |
| 7 | MCH | rs9349205 | 6 | 42033137 | A | 0.196429 | CCND3/BYSL | 0.29% | -0.0066 | 0.0008 | 1.785E-16 | -0.0037 | 0.0009 | 2.11E-05 | -0.0053 | 0.0006 | 8.198E-20 |
| 9 | MCH | rs7776054 | 6 | 135460609 | G | 0.220339 | HBS1L/MYB | 1.02% | -0.0092 | 0.0008 | 1.976E-33 | -0.0107 | 0.0009 | 4.33E-36 | -0.0099 | 0.0006 | 7.356E-69 |
| 10 | MCH | rs628751 | 6 | 139880112 | C | 0.491667 | CITED2 | 0.34% | -0.0049 | 0.0007 | 3.84E-13 | -0.0034 | 0.0008 | 7.24E-06 | -0.0043 | 0.0005 | 1.262E-17 |
| 14 | MCH | rs10758658 | 9 | 4846877 | A | 0.186441 | RCL1 | 0.18% | -0.0048 | 0.0008 | 1.634E-08 | -0.0048 | 0.0009 | 5.14E-07 | -0.0048 | 0.0006 | 2.166E-14 |
| 19 | MCH | rs1122794 | 16 | 249156 | A | 0.224138 | ITFG 3 | 0.28% | 0.0054 | 0.001 | 2.992E-08 | 0.0036 | 0.0012 | 0.00299 | 0.0047 | 0.0007 | 2.675E-10 |
| 20 | MCH | rs11085824 | 19 | 12862547 | G | 0.366667 | GCDH | 0.20% | -0.0041 | 0.0007 | 8.105E-09 | -0.003 | 0.0009 | 0.000532 | -0.0037 | 0.0005 | 1.415E-11 |
| 22 | MCH | rs2413450 | 22 | 35800170 | T | 0.381818 | TMPRSS6 | 0.41% | -0.006 | 0.0007 | 8.818E-17 | -0.0068 | 0.0008 | 5.34E-18 | -0.0064 | 0.0005 | 8.77E-34 |
| 1 | MCHC | rs857721 | 1 | 156879172 | A | 0.316667 | SPTA1 | 0.33% | -0.0022 | 0.0004 | 3.414E-09 | -0.0013 | 0.0004 | 0.00266 | -0.0018 | 0.0003 | 1.033E-10 |
| 9 | MCHC | rs9373124 | 6 | 135464902 | C | 0.220339 | HBS1L/MYB | 0.30% | -0.0023 | 0.0004 | 6.486E-10 | -0.0018 | 0.0004 | 2.6E-05 | -0.0021 | 0.0003 | 7.003E-14 |
| 3 | MCV | rs2540917 | 2 | 60462263 | C | 0.433333 | BCL11A | 0.24% | -0.0031 | 0.0005 | 2.127E-11 | -0.0022 | 0.0006 | 0.000192 | -0.0028 | 0.0004 | 1.125E-14 |
| 4 | MCV | rs9859260 | 3 | 197284944 | C | 0.35 | TFRC | 0.23% | 0.003 | 0.0005 | 3.246E-10 | 0.003 | 0.0008 | 0.000166 | 0.003 | 0.0004 | 8.499E-14 |
| 5 | MCV | rs172629 | 4 | 55102519 | G | 0.116667 | KIT | 0.27% | -0.0043 | 0.0007 | 1.36E-09 | -0.0051 | 0.001 | 2.22E-07 | -0.0046 | 0.0006 | 9.816E-16 |
| 6 | MCV | rs1800562 | 6 | 26201120 | A | 0.041667 | HFE | 0.58% | 0.0115 | 0.0011 | 1.425E-27 | 0.0137 | 0.0015 | 5.02E-20 | 0.0122 | 0.0009 | 1.012E-46 |
| 7 | MCV | rs9349205 | 6 | 42033137 | A | 0.196429 | CCND3/BYSL | 0.58% | -0.0055 | 0.0005 | 1.756E-24 | -0.0043 | 0.0008 | 8.48E-08 | -0.0051 | 0.0004 | 1.121E-31 |
| 8 | MCV | rs9374080 | 6 | 109723113 | C | 0.375 | CD164 | 0.22% | -0.0026 | 0.0005 | 3.695E-08 | -0.0017 | 0.0006 | 0.003738 | -0.0023 | 0.0004 | 4.198E-10 |
| 9 | MCV | rs4895441 | 6 | 135468266 | G | 0.225 | HBS1L/MYB | 1.12% | -0.008 | 0.0005 | 1.004E-57 | -0.0083 | 0.0008 | 3.03E-27 | -0.0081 | 0.0004 | 7.241E-86 |
| 10 | MCV | rs643381 | 6 | 139881116 | A | 0.489362 | CITED2 | 0.50% | -0.0039 | 0.0005 | 2.663E-18 | -0.0037 | 0.0007 | 1.63E-07 | -0.0039 | 0.0004 | 4.665E-25 |
| 11 | MCV | rs12718597 | 7 | 50395922 | A | 0.275 | IKZF1 | 0.26% | 0.0032 | 0.0005 | 8.138E-12 | 0.0018 | 0.0007 | 0.0145 | 0.0028 | 0.0004 | 4.689E-13 |
| 12 | MCV | rs7786877 | 7 | 100051951 | G | 0.208333 | TFR 2 | 0.13% | 0.0032 | 0.0005 | 5.452E-09 | 0.0024 | 0.0008 | 0.002081 | 0.003 | 0.0004 | 2.543E-11 |
| 14 | MCV | rs10758658 | 9 | 4846877 | A | 0.186441 | RCL1 | 0.29% | -0.0041 | 0.0006 | 4.354E-13 | -0.0045 | 0.0008 | 4.65E-08 | -0.0043 | 0.0005 | 3.184E-20 |
| 15 | MCV | rs11239550 | 10 | 45344735 | G | 0.228814 | MARCH8 | 0.15% | -0.0028 | 0.0005 | 1.873E-08 | -0.0022 | 0.0007 | 0.003496 | -0.0026 | 0.0004 | 1.346E-10 |
| 18 | MCV | rs4466998 | 14 | 64545293 | A | 0.478723 | FNTB | 0.17% | 0.0027 | 0.0005 | 8.925E-09 | 0.0008 | 0.0006 | 0.2061 | 0.002 | 0.0004 | 4.907E-08 |
| 19 | MCV | rs7189020 | 16 | 244804 | T | 0.431034 | ITFG3 | 0.19% | -0.0031 | 0.0005 | 1.081E-09 | -0.0024 | 0.0007 | 0.000871 | -0.0029 | 0.0004 | 1.819E-12 |
| 20 | MCV | rs7255045 | 19 | 12793269 | A | 0.25 | RTBDN | 0.27% | -0.0037 | 0.0006 | 1.233E-11 | -0.0018 | 0.0008 | 0.0266 | -0.0032 | 0.0004 | 2.173E-12 |
| 22 | MCV | rs2413450 | 22 | 35800170 | T | 0.381818 | TMPRSS6 | 0.65% | -0.0054 | 0.0005 | 1.078E-30 | -0.0046 | 0.0007 | 7.62E-11 | -0.0052 | 0.0004 | 2.772E-41 |
| 23 | MCV | rs131794 | 22 | 49318618 | A | 0.166667 | ECGF1 | 0.22% | -0.0044 | 0.0006 | 2.189E-13 | -0.0029 | 0.0009 | 0.001795 | -0.004 | 0.0005 | 1.033E-15 |
| 9 | RBC | rs9483788 | 6 | 135461324 | G | 0.225 | HBS1L/MYB | 0.65% | 0.0141 | 0.0016 | 3.115E-19 | 0.0155 | 0.0013 | 2.19E-30 | 0.0141 | 0.001 | 1.148E-47 |
| 12 | RBC | rs2075671 | 7 | 100183042 | A | 0.225 | EPO | 0.20% | 0.0086 | 0.0016 | 3.058E-08 | 0.0047 | 0.0016 | 0.003383 | 0.0068 | 0.0011 | 1.123E-09 |
Replication test results for the lead SNP per locus and per erythrocyte trait (45 SNPs). Results are organized by trait, the by locus, as indicated in Table 1. Results from a combined CHARGE and HaemGen Consortium meta-analysis are presented. Minor allele frequency (MAF) is presented based on HapMap CEU. % Var indicates the percent of variance explained by the lead SNP in the corresponding trait-locus. P values in bold font meet a Bonferroni-corrected significance threshold for replication of P < 0.0011 (0.05/45). Units were Hgb g/dl, Hct %, MCH picogram, MCHC g/dL, MCV femtoliter, RBC 1 M cells/ccm.