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. 2022 Mar 11;3(2):100099. doi: 10.1016/j.xhgg.2022.100099

Table 2.

Novel loci and new signals in established loci by trait from a trans-ancestral meta-analysis of adult samples from the HISLA, AAAGC, and GIANT consortia

Trait SNP rsid Chr Position (hg19) Locus namec Effect/other alleles EAF
 N Unconditioned meta-analysis results
 Conditioned on all known SNPs within 10 Mb region
 UKBB (validation results)
HISLA AAAGC GIANT Beta SE p value HetISq Beta SE p value EAF N Beta SE p value
Novel locia
BMI rs4675117 2 227769794 RHBDD1 T/C 0.421 0.104 0.383 343,628 0.017 0.003 8.56 × 10−8 0 0.019 0.003 2.23 × 10−9 0.383 336,107 0.006 0.002 1.82 × 10−2
BMI rs9860730 3 64701146 ADAMTS9-AS2 A/G 0.354 0.222 0.767 428,763 −0.016 0.003 1.67 × 10−8 0 −0.015 0.003 3.80 × 10−8 0.712 336,107 −0.008 0.003 4.54 × 10−3
BMI rs150992 5 98275197 CHD1-DT A/G 0.778 0.645 0.700 439,077 0.018 0.003 5.40 × 10−10 0 0.017 0.003 1.02 × 10−8 0.693 336,107 0.005 0.003 3.74 × 10−2
Height rs17375290 1 61334177 NFIA A/G 0.830 0.645 0.793 364,636 0.017 0.003 3.47 × 10−8 0 0.017 0.003 3.00 × 10−8 0.794 336,474 0.002 0.002 4.58 × 10−1
Height rs10737541 1 168214098 ANKRD36BP1 T/G 0.399 0.645 0.196 319,809 −0.018 0.003 1.60 × 10−9 0 −0.018 0.003 3.16 × 10−10 0.226 336,474 −0.004 0.002 4.37 × 10−2
Height rs4618485 6 73555917 KCNQ5 A/G 0.750 0.645 0.592 348,626 0.014 0.003 4.72 × 10−8 39.2 0.018 0.003 4.34 × 10−12 0.604 336,474 0.003 0.002 7.02 × 10−2
Height rs17493997 8 82044302 PAG1 C/G 0.493 0.645 0.340 325,906 −0.015 0.003 3.42 × 10−8 0 −0.017 0.003 2.73 × 10−10 0.299 336,474 −0.0003 0.002 8.56 × 10−1
WHRadjBMI (sex combined) rs16873543 6 45577134 RUNX2 T/C 0.716 0.645 0.767 209,552 −0.018 0.004 3.20 × 10−6 0 −0.022 0.004 9.65 × 10−9 0.724 484,563 −0.008 0.002 5.50 × 10−4
New signals in established locib
BMI rs10540 11 494662 RNH1 A/G 0.200 0.031 0.092 470,714 −0.021 0.004 1.01 × 10−7 0 −0.023 0.004 5.75 × 10−9 0.135 336,107 −0.007 0.004 4.16 × 10−2
BMI rs4807179 19 1956035 CSNK1G2 A/G 0.494 0.218 0.525 309,507 0.020 0.003 2.75 × 10−10 0 0.018 0.003 1.52 × 10−8 0.632 336,107 0.014 0.002 1.06 × 10−8
BMI rs4813428 20 21451848 NKX2-2 T/C 0.181 0.093 0.108 321,797 0.029 0.005 2.89 × 10−10 0 0.029 0.005 1.46 × 10−10 0.093 336,107 0.013 0.004 2.47 × 10−3
Height rs4912122 1 19876438 NKX2-2 A/G 0.383 0.837 0.383 334,951 −0.015 0.003 6.33 × 10−9 0 −0.019 0.003 1.45 × 10−13 0.350 336,474 −0.012 0.002 1.58 × 10−11
Height rs4425978 1 42243878 HIVEP3 T/C 0.389 0.189 0.580 351,587 0.014 0.003 2.14 × 10−8 0 0.016 0.003 3.63 × 10−10 0.533 336,474 0.008 0.002 5.41 × 10−6
Height rs618555 1 86481084 COL24A1 T/C 0.241 0.064 0.353 320,239 0.019 0.003 5.47 × 10−12 0 0.016 0.003 2.90 × 10−8 0.311 336,474 0.008 0.002 1.67 × 10−5
Height rs6545538 2 56217900 MIR216A A/G 0.258 0.628 0.258 305,704 0.022 0.003 1.23 × 10−13 0 0.019 0.003 2.59 × 10−11 0.266 336,474 0.011 0.002 1.25 × 10−8
Height rs2741311 2 233239743 ALPP T/C 0.076 0.018 0.050 463,609 0.046 0.005 1.41 × 10−21 49.6 0.030 0.005 4.78 × 10−10 0.080 336,474 0.033 0.003 2.39 × 10−24
Height rs6935954 6 26255451 HIST1H2BH A/G 0.306 0.103 0.408 345,378 0.042 0.003 3.06 × 10−59 46.5 0.018 0.003 3.29 × 10−12 0.425 336,474 −0.027 0.002 1.10 × 10−54
Height rs6900530 6 35280971 DEF6 T/C 0.094 0.385 0.042 123,137 −0.057 0.005 3.09 × 10−28 79.0 −0.036 0.005 6.75 × 10−12 0.027 336,474 −0.073 0.005 1.03 × 10−42
Height rs9472006 6 43067487 PTK7 A/G 0.149 0.249 0.059 212,931 −0.027 0.005 4.37 × 10−9 0 −0.034 0.005 7.04 × 10−14 0.041 336,474 −0.013 0.004 2.86 × 10−3
Height rs3822957 6 76607280 MY O 6 A/G 0.173 0.538 0.158 279,818 −0.023 0.003 4.88 × 10−12 84.4 −0.023 0.003 3.44 × 10−12 0.142 336,474 −0.015 0.002 1.98 × 10−9
Height rs1342330 6 144065685 PHACTR2 A/T 0.601 0.738 0.508 353,259 0.014 0.003 1.70 × 10−8 0 0.017 0.003 6.95 × 10−12 0.520 336,474 0.006 0.002 8.84 × 10−4
Height rs6936615 6 154355100 OPRM1 A/G 0.887 0.901 0.850 415,248 −0.018 0.003 2.47 × 10−8 0 −0.020 0.003 2.33 × 10−9 0.830 336,474 −0.003 0.002 1.73 × 10−1
Height rs991946 6 166329862 RP11-252P19.3c T/C 0.481 0.486 0.500 379,912 −0.019 0.002 1.28 × 10−14 36.7 −0.019 0.002 9.96 × 10−15 0.479 336,474 −0.013 0.002 3.92 × 10−13
Height rs7816300 8 109787856 TMEM74 T/C 0.262 0.116 0.260 397,735 −0.015 0.003 2.24 × 10−8 0 −0.016 0.003 5.47 × 10−9 0.299 336,474 −0.002 0.002 3.94 × 10−1
Height rs4520250 9 88924057 TUT7 A/C 0.235 0.069 0.433 295,945 0.015 0.003 3.80 × 10−8 55.9 0.016 0.003 1.48 × 10−8 0.339 336,474 0.010 0.002 4.36 × 10−8
Height rs7029157 9 97000863 snoU13c T/C 0.084 0.325 0.067 262,808 0.028 0.004 5.85 × 10−11 16.8 0.026 0.004 1.00 × 10−9 0.088 336,474 0.030 0.003 4.55 × 10−22
Height rs12347744 9 97575273 AOPEP T/C 0.102 0.015 0.033 454,111 −0.032 0.005 6.55 × 10−11 65.8 −0.030 0.005 6.06 × 10−10 0.061 336,474 −0.031 0.004 1.04 × 10−17
Height rs7024254 9 109498129 ZNF462 A/G 0.255 0.721 0.207 324,351 0.017 0.003 1.04 × 10−8 23.7 0.036 0.003 6.10 × 10−35 0.204 336,474 0.010 0.002 6.50 × 10−6
Height rs10119624 9 118305438 DELEC1 A/G 0.612 0.437 0.683 353,374 0.021 0.003 2.56 × 10−16 31.1 0.022 0.003 8.02 × 10−17 0.671 336,474 0.012 0.002 3.20 × 10−10
Height rs2902635 10 105476045 SH3PXD2A T/G 0.710 0.382 0.821 308,782 −0.021 0.003 1.59 × 10−12 0 −0.017 0.003 1.62 × 10−8 0.805 336,474 −0.015 0.002 7.65 × 10−12
Height rs17659078 11 2284590 ASCL2 A/C 0.211 0.149 0.258 354,931 0.019 0.003 1.78 × 10−10 9.0 0.016 0.003 3.45 × 10−8 0.273 336,474 0.004 0.002 2.24 × 10−2
Height rs11605693 11 122837037 JHY T/C 0.591 0.384 0.448 380,447 −0.017 0.002 3.44 × 10−12 0 −0.018 0.002 3.07 × 10−14 0.447 336,474 −0.013 0.002 4.45 × 10−13
Height rs621794 11 125849462 CDON A/G 0.500 0.430 0.475 380,049 −0.014 0.002 1.46 × 10−8 0 −0.014 0.002 7.29 × 10−9 0.429 336,474 −0.009 0.002 1.76 × 10−7
Height rs11221442 11 128577624 FLI1 C/G 0.171 0.109 0.217 352,360 −0.022 0.003 2.03 × 10−12 78.8 −0.023 0.003 2.03 × 10−13 0.252 336,474 −0.008 0.002 2.59 × 10−5
Height rs12300112 12 103147575 LINC00485 C/G 0.075 0.242 0.008 154,014 0.041 0.006 4.31 × 10−13 45.2 0.038 0.006 3.11 × 10−11 0.027 336,474 0.038 0.005 4.61 × 10−12
Height rs11616067 12 116393174 MED13L A/G 0.841 0.904 0.750 327,941 0.021 0.003 6.38 × 10−12 21.0 0.018 0.003 2.80 × 10−9 0.768 336,474 0.012 0.002 6.01 × 10−9
Height rs17197170 14 21977962 METTL3 A/G 0.931 0.960 0.842 310,344 −0.026 0.004 5.40 × 10−12 64.9 −0.025 0.004 3.74 × 10−11 0.828 336,474 −0.018 0.002 3.07 × 10−14
Height rs11076551 16 51109492 RP11-883G14.4c A/G 0.341 0.343 0.267 434,688 0.014 0.003 2.14 × 10−8 21.6 0.015 0.003 5.87 × 10−9 0.376 336,474 0.009 0.002 2.51 × 10−7
Height rs12918773 16 89741403 SPATA33 A/G 0.121 0.036 0.149 279,104 −0.024 0.004 7.45 × 10−9 46.1 −0.024 0.004 3.50 × 10−9 0.112 336,474 −0.024 0.003 4.71 × 10−19
Height rs1346490 19 7244233 INSR A/C 0.546 0.611 0.500 333,896 0.015 0.003 3.99 × 10−9 12.3 0.014 0.003 4.86 × 10−8 0.620 336,474 0.009 0.002 1.67 × 10−7
Height rs17457472 19 17493610 PLVAP A/C 0.037 0.062 0.028 356,712 −0.051 0.007 5.70 × 10−14 0 −0.042 0.007 9.89 × 10−10 0.040 336,474 −0.019 0.004 1.12 × 10−5
WHRadjBMI (sex combined) rs17099388 5 142095250 FGF1 A/G 0.166 0.256 0.008 105,460 0.039 0.007 3.14 × 10−9 0 0.037 0.007 2.47 × 10−8 0.041 484,563 0.025 0.005 2.00 × 10−7
WHRadjBMI (sex combined) rs7975017 12 26428793 SSPN T/C 0.303 0.717 0.167 267,044 −0.021 0.004 7.57 × 10−9 5.5 −0.021 0.004 1.05 × 10−8 0.239 484,563 −0.014 0.002 2.00 × 10−9

Chr, chromosome; EAF, effect allele frequency; HetIsq, heterogeneity I2; N, sample size; WHRadjBMI, waist-to-hip ratio adjusted for BMI; AAAGC, African American Anthropometry Genetics Consortium; GIANT, Genetic Investigation of Anthropometric Traits Consortium.

a

Each novel locus was defined by the absence of known (previously published) SNPs within 1 Mb (±500 kb) of the lead SNP.

b

Each known locus was defined by a 1 Mb region around previously identified SNP(s) for the indicated trait; the known SNP(s), p < 5 × 10−8, at each established locus can be found in Table S16.

c

Human Genome Organisation approved gene names, unless otherwise indicated.