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Table 3 SNPs present in each of the component phenotypes in compound sets, with composite p-value computed from individual phenotype components, pattern p-value computed on the compound phenotype members, odds ratio logistic regression associations GWAS for each phenotype set. Entries show locus w/ minor allele, and the odds ratio, 95 % confidence interval, and p-value for the SNP vs. the phenotype

From: Characterizing redescriptions using persistent homology to isolate genetic pathways contributing to pathogenesis

Locus Composite Pattern DxT2D DxHT DxCAD
Minor Allele p-value p-value    Age ≥ 60
rs12101936 1.079×10−9 4.961×10−5 0.76 0.78 0.80
A    (0.64–0.89) (0.67–0.90) (0.69–0.93)
    0.000628 0.000615 0.002796
rs17107637 1.872×10−8 0.002181 1.41 1.37 1.29
G    (1.14–1.75) (1.13–1.67) (1.06–1.57)
    0.00135 0.00140 0.00992
rs3759658 8.914×10−8 0.0304 1.34 1.33 1.35
A    (1.08–1.66) (1.09–1.61) (1.11–1.65)
    0.00733 0.00455 0.00267
rs6926556 9.205×10−9 0.0341 0.74 0.72 0.76
C    (0.60–0.91) (0.60–0.86) (0.63–0.92)
    0.00438 0.000457 0.00460
rs8113086 2.853×10−7 0.0936 0.75 0.77 0.75
T    (0.60–0.93) (0.64–0.93) (0.62–0.92)
    0.00841 0.00760 0.00447
rs878643 4.254×10−8 0.04394 0.764 0.800 0.819
A    (0.65–0.90) (0.69–0.93) (0.70–0.96)
    0.00841 0.00760 0.00447
rs11880382 1.518×10−7 0.005167 0.733 0.901 0.889
C    (0.64–0.84) (0.79–1.03) (0.78–1.01)
    1.669×10−5 0.118 0.077
rs2088354 3.133×10−8 0.0144 1.679 1.357 1.175
T    (1.31–2.15) (1.09–1.68) (0.95–1.46)
    3.856×10−5 0.00557 0.146
rs2992100 4.162×10−8 0.06262 0.559 0.772 1.282
A    (0.43–0.73) (0.60–0.99) (1.00–1.64)
    2.35×10−5 0.0379 0.0468
rs3781788 4.837×10−8 0.001568 1.907 1.015 1.436
T    (1.44–2.52) (0.77–1.34) (1.09–1.89)
    5.527×10−6 0.913 0.00959
rs6080252 6.587×10−8 0.002838 1.623 1.303 1.279
A    (1.28–2.06) (1.03–1.65) (1.02–1.61)
    6.277×10−5 0.0284 0.0370
rs6984384 3.906×10−8 4.502×10−5 0.742 0.840 0.895
T    (0.65–0.86) (0.74–0.96) (0.79–1.02)
    4.886×10−5 0.008405 0.09511
rs701133 3.865×10−7 0.002081 1.547 1.206 1.160
T    (1.25–1.91) (1.00–1.46) (0.96–1.41)
    5.57×10−5 0.054 0.129
rs3019548 3.905×10−7 0.009792 1.541 1.483
G    (1.20–1.98) (1.18–1.86)  
    0.000643 0.000607  
rs6807700 1.061×10−7 0.0002289 1.46 1.49
C     (1.18–1.80) (1.20–1.85)
     0.000400 0.000265
rs17077265 2.80144×10−7 0.0131 1.409 1.062
T     (1.23–1.61) (0.93–1.21)
     7.423×10−7 0.377
rs522264 2.53×10−7 2.238×10−5 0.638 0.734
T     (0.51–0.79) (0.59–0.91)
     5.567×10−5 0.00455
rs6727857 4.819×10−7 0.000935 0.660 0.932
G     (0.56–0.78) (0.79–1.10)
     1.173×10−6 0.411
  1. Genome wide p-value threshold =6.338×10−7