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. 2017 May 26;8:15606. doi: 10.1038/ncomms15606

Table 2. Summary of novel association signals.

Variant and cohorts Trait Chr:pos (EA/NEA) Nearest gene Internal replication EAF Beta (SE) P-value Overall MAC (N)
        Replication cohorts EAF Beta (SE) P-value MAC (N)        
chr16:70790626 MANOLIS HDL 16:70790626 (T/C) VAC14-AS1 VAC14 MANOLIS CoreExome 0.003 −1.885 (0.994) 5.76 × 10−2 1.26 (210) 0.006 −1.713 (0.254) 1.57 × 10−11 20 (1476)
        MANOLIS OmniExome 0.007 −1.702 (0.263) 1.81 × 10−10 17.6 (1255)        
                         
rs145556679 MANOLIS TG 11:117643264 (C/G) DSCAML1 MANOLIS CoreExome 0.005 −1.293 (0.729) 7.85 × 10−2 2.09 (209) 0.013 −1.134 (0.17) 2.53 × 10−11 49 (1476)
        MANOLIS OmniExome 0.014 −1.125 (0.175) 1.70 × 10−10 35.1 (1252)        
  VLDL     MANOLIS CoreExome 0.005 −1.365 (0.727) 6.21 × 10−2 2.1 (210) 0.013 −1.131 (0.17) 2.90 × 10−11  
        MANOLIS OmniExome 0.014 −1.118 (0.175) 2.29 × 10−10 35.1 (1253)        
                         
rs140087759 MANOLIS WHR 5:28292892 (T/C) CTD-2061E9.1 MANOLIS CoreExome 0.015 1.676 (0.411) 5.92 × 10−5 6.12 (204) 0.01 1.189 (0.209) 1.35 × 10−8 31 (1476)
        MANOLIS OmniExome 0.009 1.02 (0.243) 2.90 × 10−5 18.8 (1047)        
                         
rs13382259* Pomak DBP 2:113934176 (T/A) PSD4 Pomak CoreExome 0.047 0.509 (0.126) 6.98 × 10−5 60.3 (641) 0.043 0.554 (0.1) 3.18 × 10−8 172 (1737)
        Pomak OmniExome 0.039 0.629 (0.164) 1.36 × 10−4 43 (551)        
                         
rs6131100* Pomak FGBMIadj 20:10434530 (A/T) SLX4IP Pomak CoreExome 0.038 −0.573 (0.16) 3.62 × 10−4 43.2 (569) 0.037 −0.79 (0.139) 1.21 × 10−8 135 (1737)
        Pomak OmniExome 0.035 −1.454 (0.279) 7.12 × 10−7 12.2 (174)        
                         
rs79748197 Pomak WBC 2:19430105 (G/A) AC092594.1 Pomak CoreExome 0.004 −1.242 (0.403) 2.12 × 10−3 5.8 (725) 0.008 −1.156 (0.209) 3.00 × 10−8 31 (1737)
        Pomak OmniExome 0.004 −1.125 (0.243) 4.14 × 10−6 20.9 (948)        
                         
rs557129696 Pomak HGB 11:5328683 (G/T) HBG2 HBE1 AC104389.28 Pomak CoreExome 0.002 −1.95 (0.606) 1.36 × 10−3 2.87 (717) 0.004 −2.027 (0.308) 4.83 × 10−11 13 (1737)
        Pomak OmniExome 0.005 −2.054 (0.358) 1.30 × 10−8 9.45 (945)        
                         
rs112037309* MANOLIS & Pomak Weight 4:106617136 (A/G) ARHGEF38 INTS12 MANOLIS 0.075 0.295 (0.078) 1.43 × 10−4 189.8 (1258) 0.075 0.287 (0.052) 2.70 × 10−8 485 (3213)
        Pomak 0.075 0.28 (0.07) 5.96 × 10−5 250.8 (1672)        

All variants are intronic with the exception of rs140087759 which is intergenic, variant consequences are taken from Ensembl (http://www.ensembl.org). For the internal replication the software used was GEMMA with the exception of rs112037309 in which METACARPA was used. Cohorts, cohorts from which the signal arose. Chr:pos, represents the chromosome and position in GRCh37/hg19 coordinates; EA, effect allele; NEA, non-effect allele; EAF, effect allele frequency; P-value, the likelihood ratio test P-value from GEMMA or Wald test P-value from METACARPA; MAC, minor allele count for samples in the analysis; Overall MAC, minor allele count for all samples in the cohorts from which the signal arose, established using the rounded imputed allele dosages from SNPTEST (https://mathgen.stats.ox.ac.uk/genetics_software/snptest/snptest.html); N, sample size; HDL, high-density lipoprotein cholesterol; DBP, diastolic blood pressure; TG, triglycerides; VLDL, very low-density lipoprotein cholesterol; FGBMIadjusted, fasting glucose adjusted for body mass index; HGB, haemoglobin; WBC, white blood cells; WHR, waist-to-hip ratio.

*At least one proxy is present in the International HapMap project data (http://hapmap.ncbi.nlm.nih.gov). Proxies were determined using LD (r2>0.8 in the cohorts used for the meta-analysis) for each novel variant. If a proxy was in HapMap it also had high LD (r2>0.9) with the variant in the 1000 Genomes Project CEU population3. LocusZoom was used to create the regional plots (http://csg.sph.umich.edu/locuszoom/).