Table 2.
Variants Associated with White Blood Cell Traits
| Trait (Population) | dbSNPID | Chr | Pos | Alt/Ref | EAF | Gene | Annotation | AA Substitution |
Discovery |
Replication |
Combined Meta-analysis |
|||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| N | Beta (SE) | p | N | EAF | Beta (SE) | p | N | EAF | Beta (SE) | p | phet | |||||||||
| WBC (EA) | rs1260326 | 2 | 27,730,940 | C/T | 0.58 | GCKR | missense, splice site | p.Leu446Pro | 108,596 | −0.030 (0.005) | 4.01 × 10−10 | 17,897 | 0.6 | −0.044 (0.012) | 2.66 × 10−4 | 126,493 | 0.58 | −0.032 (0.004) | 8.13 × 10−13 | 0.28 |
| WBC (All) | rs2276853 | 3 | 47,282,303 | A/G | 0.58 | KIF9 | missense | p.Arg573Trp | 132,764 | 0.023 (0.004) | 3.65 × 10−8 | 17,897 | 0.6 | 0.025 (0.012) | 3.00 × 10−2 | 150,661 | 0.58 | 0.023 (0.004) | 3.29 × 10−9 | 0.86 |
| WBC (All) | rs185819a | 6 | 32,050,067 | C/T | 0.51 | TNXB | missense | p.His1161Arg | 132,764 | 0.031 (0.005) | 4.02 × 10−10 | 17,897 | 0.47 | 0.034 (0.015) | 2.24 × 10−2 | 150,661 | 0.51 | 0.031 (0.005) | 2.85 × 10−11 | 0.83 |
| WBC (All) | rs9374080 | 6 | 109,616,420 | C/T | 0.43 | CCDC162P | intronic regulatory | 132,764 | 0.023 (0.004) | 4.01 × 10−8 | 17,897 | 0.46 | 0.025 (0.011) | 2.55 × 10−2 | 150,661 | 0.43 | 0.023 (0.004) | 3.15 × 10−9 | 0.84 | |
| WBC (EA) | rs3747869 | 10 | 73,520,632 | C/A | 0.9 | C10orf54 (DD1a) | missense | p.Asp187Glu | 108,596 | 0.040 (0.007) | 4.26 × 10−8 | 17,897 | 0.9 | 0.083 (0.018) | 6.40 × 10−6 | 126,493 | 0.9 | 0.046 (0.007) | 1.42 × 10−11 | 0.03 |
| WBC (EA) | rs1935 | 10 | 64,927,823 | G/C | 0.49 | JMJD1C | missense | p.Glu2353Asp | 108,596 | −0.026 (0.005) | 2.46 × 10−8 | 17,897 | 0.46 | −0.027 (0.012) | 2.06 × 10−2 | 126,493 | 0.49 | −0.026 (0.004) | 1.57 × 10−9 | 0.93 |
| WBC (EA) | rs1292053 | 17 | 57,963,537 | G/A | 0.45 | TUBD1 | missense | p.Met76Thr | 108,596 | −0.03 (0.004) | 1.28 × 10−11 | 17,897 | 0.44 | −0.027 (0.011) | 1.51 × 10−2 | 126,493 | 0.45 | −0.030 (0.004) | 6.55 × 10−13 | 0.78 |
| WBC (EA) | rs4760 | 19 | 44,153,100 | G/A | 0.16 | CD87 (PLAUR) | missense | p.Leu272Pro | 85,685 | −0.043 (0.007) | 2.51 × 10−10 | 17,897 | 0.15 | −0.052 (0.015) | 7.13 × 10−4 | 103,582 | 0.16 | −0.044 (0.006) | 8.34 × 10−13 | 0.6 |
| WBC (EA) | rs3865444 | 19 | 51,727,962 | A/C | 0.31 | CD33 | upstream | 86,936 | −0.037 (0.005) | 3.51 × 10−12 | 17,897 | 0.32 | −0.033 (0.012) | 5.14 × 10−3 | 104,833 | 0.31 | −0.036 (0.005) | 6.81 × 10−14 | 0.77 | |
| WBC (All) | rs2836878 | 21 | 40,465,534 | A/G | 0.26 | ETS2-PSMG1 | intergenic | 132,764 | −0.025 (0.005) | 8.36 × 10−8 | 17,897 | 0.26 | −0.026 (0.012) | 3.44 × 10−2 | 150,661 | 0.26 | −0.025 (0.004) | 8.41 × 10−9 | 0.89 | |
| NEU (EA) | rs3747869 | 10 | 73,520,632 | C/A | 0.9 | C10orf54 (DD1a) | missense | p.Asp187Glu | 60,851 | 0.053 (0.010) | 2.11 × 10−8 | 16,669 | 0.9 | 0.073 (0.019) | 1.17 × 10−4 | 77,520 | 0.9 | 0.057 (0.009) | 1.65 × 10−11 | 0.34 |
| NEU (EA) | rs4760 | 19 | 44,153,100 | G/A | 0.16 | CD87 (PLAUR) | missense | p.Leu272Pro | 56,112 | −0.047 (0.008) | 1.54 × 10−8 | 16,669 | 0.15 | −0.044 (0.016) | 5.55 × 10−3 | 72,781 | 0.16 | −0.046 (0.007) | 3.01 × 10−10 | 0.87 |
| MON (All) | rs4917014 | 7 | 50,305,863 | G/T | 0.28 | C7orf72-IKZF1 | intergenic | 57,183 | −0.038 (0.007) | 1.97 × 10−8 | 16,669 | 0.32 | −0.048 (0.012) | 8.92 × 10−5 | 73,852 | 0.29 | −0.040 (0.006) | 9.75 × 10−12 | 0.48 | |
| MON (EA) | rs11625112 | 14 | 23,596,740 | G/A | 0.46 | SLC7A8 | intronic | 44,325 | −0.038 (0.007) | 3.82 × 10−8 | 16,669 | 0.45 | −0.031 (0.012) | 7.04 × 10−3 | 60,994 | 0.46 | −0.036 (0.006) | 1.03 × 10−9 | 0.62 | |
| MON (EA) | rs11642873a | 16 | 85,991,705 | C/A | 0.2 | IRF8-LINC01082 | intergenic | 44,325 | 0.057 (0.008) | 1.41 × 10−11 | 16,669 | 0.2 | 0.113 (0.014) | 6.17 × 10−15 | 60,994 | 0.2 | 0.072 (0.007) | 1.40 × 10−22 | 0.001 | |
| MON (All) | rs1292053 | 17 | 57,963,537 | G/A | 0.45 | TUBD1 | missense | p.Met76Thr | 57,183 | −0.036 (0.006) | 2.55 × 10−9 | 16,669 | 0.44 | −0.040 (0.012) | 6.08 × 10−4 | 73,852 | 0.45 | −0.037 (0.005) | 6.53 × 10−12 | 0.76 |
| LYM (EA) | rs2229094 | 6 | 31,540,556 | C/T | 0.26 | LTA | missense | p.Cys13Arg | 47,105 | 0.046 (0.008) | 1.89 × 10−8 | 16,711 | 0.25 | 0.078 (0.018) | 8.54 × 10−6 | 63,816 | 0.26 | 0.051 (0.007) | 3.14 × 10−12 | 0.09 |
| LYM (EA) | rs4763879 | 12 | 9,910,164 | A/G | 0.36 | CD69 | intronic regulatory | 47,105 | −0.038 (0.007) | 3.08 × 10−8 | 16,711 | 0.36 | −0.038 (0.012) | 1.36 × 10−3 | 63,816 | 0.36 | −0.038 (0.006) | 1.59 × 10−10 | 0.99 | |
| BAS (EA) | rs2295764 | 20 | 31,025,163 | G/A | 0.36 | ASXL1 | 3′ UTR | 44,138 | −0.042 (0.007) | 3.28 × 10−9 | 15,770 | 0.36 | −0.031 (0.012) | 9.78 × 10−3 | 59,908 | 0.36 | −0.039 (0.006) | 1.46 × 10−10 | 0.43 | |
Abbreviations are as follows: Chr, chromosome; Pos, basepair position; Alt, effect allele; Ref, reference allele; EAF, effect allele frequency; AA, amino acid; phet, p value for heterogeneity; EA, European ancestry; All, combined European, African, Hispanic American, East Asian, and South Asian ancestries; WBC, white blood cell; NEU, neutrophil; MON, monocyte; LYM, lymphocyte; BAS, basophil.
a
Secondary signal identified through conditional analysis.