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Table 3 SNPs associated disease severity at FDR less than 0.02

From: Genetic modifiers of Hb E/β0 thalassemia identified by a two-stage genome-wide association study

        Disease Severity   HbF%  
SNP Chr BP Gene Min Maj MAF OR P Bonf FDR Beta SE P Var
rs483850 1 203478366 FAIM3 T A 0.45 0.65 9.7E-04 7.3E-01 0.01 0.05 .05 0.10 .52
rs934956 2 104555647 Intergenic T C 0.17 1.93 5.6E-04 4.2E-01 0.01 0.00 .05 0.97 .40
rs370898 3 21442705 ZNF659 G T 0.05 0.37 1.4E-03 1 0.01 0.01 .05 0.93 .32
rs903047 3 132234707 NEK11 T C 0.35 1.58 1.5E-03 1 0.01 -0.03 .05 0.44 .30
rs6443662 3 180834067 Intergenic C T 0.29 0.58 3.8E-04 2.8E-01 0.005 0.02 .05 0.57 .30
rs950310 4 9519119 SLC2A9 A T 0.17 2.03 3.5E-04 2.6E-01 0.005 -0.08 .05 0.18 .29
rs258824 5 142577483 ARHGAP26 A G 0.39 1.58 1.1E-03 8.3E-01 0.01 -0.06 .05 0.12 .29
rs234915 6 2154576 GMDS A C 0.21 0.52 1.3E-04 9.5E-02 0.002 0.03 .05 0.45 .27
rs545537 6 117751734 ROS1 A G 0.17 1.90 8.4E-04 6.3E-01 0.01 0.03 .04 0.59 .27
rs4376364 6 135349178 HBS1L G T 0.34 1.70 4.3E-04 3.2E-01 0.01 -0.07 .05 0.10 .27
rs7804867 7 102627708 SLC26A5 A G 0.28 1.76 3.4E-04 2.6E-01 0.005 -0.03 .05 0.51 .27
rs6972505 7 102657988 SLC26A5 C G 0.24 2.13 7.6E-06 5.8E-03 0.0001 -0.04 .05 0.35 .27
rs1563408 7 113897140 FOXP2 G A 0.49 1.63 4.1E-04 3.1E-01 0.01 0.02 .05 0.52 .27
rs766003 9 69709994 c9orf135 G A 0.16 0.52 2.6E-04 1.9E-01 0.004 0.04 .05 0.37 .25
rs7936823 11 5206792 Intergenic C T 0.42 0.23 2.0E-11 1.5E-08 <.0001 0.10 .05 0.04 .25
rs6578588 11 5208867 Intergenic A G 0.42 0.21 1.2E-11 9.0E-09 <.0001 0.09 .05 0.07 .24
rs3813727 11 5212511 HBD T C 0.42 0.24 8.6E-11 6.5E-08 <.0001 0.10 .05 0.04 .23
rs3759074 11 5214371 Intergenic T C 0.41 0.18 3.6E-13 ± 2.7E-10 <.0001 0.10 .05 0.05 .23
rs10837643 11 5214635 Intergenic A T 0.43 0.22 5.4E-10 4.1E-07 <.0001 0.14 .05 0.002 .23
rs4320977 11 5214758 Intergenic T C 0.42 0.23 1.6E-11 1.2E-08 <.0001 0.10 .05 0.04 .22
rs3759073 11 5214862 Intergenic A G 0.42 0.22 2.5E-11 1.9E-08 <.0001 0.09 .05 0.07 .22
rs4402323 11 5215185 Intergenic G A 0.42 0.22 4.5E-12 3.4E-09 <.0001 0.10 .05 0.04 .22
rs4910543 11 5215423 Intergenic C G 0.42 0.22 5.8E-12 4.4E-09 <.0001 0.10 .05 0.04 .22
rs2105819 11 5216332 Intergenic C G 0.42 0.24 4.9E-11 3.7E-08 <.0001 0.11 .05 0.03 .22
rs10128556 11 5220248 HBBP1 A G 0.42 0.20 3.4E-13 2.6E-10 <.0001 0.10 .05 0.05 .21
rs2071348 11 5220725 HBBP1 C A 0.41 0.19 4.8E-13 3.6E-10 <.0001 0.09 .05 0.07 .21
rs11036431 11 5222255 HBBP1 T C 0.43 0.23 6.3E-12 4.8E-09 <.0001 0.08 .05 0.10 .20
rs916111 11 5225911 HBG1 A T 0.43 0.23 1.7E-11 1.3E-08 <.0001 0.10 .05 0.04 .20
rs2855038 11 5228721 HBG1 A G 0.43 0.24 4.5E-12 3.4E-09 <.0001 0.10 .05 0.04 .19
rs2855036 11 5229250 HBG2 A G 0.41 0.20 3.5E-13 2.6E-10 <.0001 0.09 .05 0.08 .19
rs2855126 11 5229721 HBG2 G C 0.43 0.24 7.0E-12 5.3E-09 <.0001 0.10 .05 0.03 .18
rs2855125 11 5230257 HBG2 A C 0.43 0.25 1.2E-11 8.8E-09 <.0001 0.12 .04 0.01 .18
rs2236794 11 5230843 HBG2 G A 0.42 0.24 2.5E-11 1.9E-08 <.0001 0.09 .05 0.07 .17
rs2070972 11 5231293 HBG2 T G 0.43 0.24 3.6E-12 2.7E-09 <.0001 0.10 .03 0.04 .16
rs2187608 11 5231423 HBG2 G C 0.41 0.20 7.0E-13 5.3E-10 <.0001 0.09 .04 0.06 .16
rs2070973 11 5231985 HBG2 A G 0.44 0.23 5.6E-12 4.2E-09 <.0001 0.09 .05 0.06 .16
rs7482144 (XmnI) 11 5232745 HBG2 T C 0.42 0.20 3.7E-13 2.8E-10 <.0001 0.07 .05 0.17 .15
rs2011051 11 5233395 HBG2 C A 0.43 0.24 1.2E-11 9.1E-09 <.0001 0.09 .05 0.07 .15
rs2855123 11 5233652 HBG2 T A 0.44 0.24 4.9E-11 3.7E-08 <.0001 0.07 .05 0.14 .14
rs2855121 11 5233869 HBG2 A G 0.41 0.20 2.2E-12 1.7E-09 <.0001 0.08 .05 0.12 .12
rs10160820 11 5239027 Intergenic G T 0.42 0.19 4.7E-13 3.6E-10 <.0001 0.09 .05 0.09 .12
rs7480802 11 5239080 Intergenic A G 0.43 0.24 2.1E-11 1.6E-08 <.0001 0.09 .05 0.07 .11
rs10160747 11 5240751 Intergenic A G 0.42 0.20 1.5E-12 1.2E-09 <.0001 0.09 .06 0.08 .11
rs10837707 11 5243234 HBE1 A G 0.43 0.22 1.4E-12 1.0E-09 <.0001 0.09 .05 0.07 .11
rs4910740 11 5243705 HBE1 C T 0.42 0.21 9.9E-13 7.5E-10 <.0001 0.10 .05 0.06 .11
bg200 * 11 5245549 HBE1 T G 0.41 0.18 2.6E-13 2.0E-10 <.0001 0.10 .04 0.07 .10
rs3834466 11 5247976 HBE1 C A 0.42 0.23 1.7E-11 1.2E-08 <.0001 0.07 .05 0.13 .10
rs3759070 11 5248038 HBE1 C G 0.41 0.21 1.5E-12 1.1E-09 <.0001 0.08 .04 0.09 .08
rs3759069 11 5248240 HBE1 T C 0.43 0.23 3.1E-12 2.4E-09 <.0001 0.09 .06 0.06 .08
rs11036562 11 5250549 HBE1 G T 0.48 0.38 2.7E-08 2.0E-05 <.0001 0.07 .05 0.12 .08
rs11036634 11 5265154 Intergenic A G 0.50 2.34 1.4E-06 1.0E-03 <.0001 -0.02 .06 0.65 .07
bg12 * 11 5266933 Intergenic G T 0.49 2.31 6.8E-07 5.1E-04 <.0001 -0.06 .05 0.20 .06
rs11036639 11 5267001 Intergenic C T 0.46 0.34 6.0E-09 4.5E-06 <.0001 0.06 .04 0.21 .06
rs11036641 11 5267496 Intergenic A T 0.49 2.26 2.6E-06 2.0E-03 <.0001 -0.06 .04 0.21 .06
rs11036644 11 5268836 Intergenic C T 0.49 2.26 1.5E-06 1.2E-03 <.0001 -0.06 .05 0.18 .06
rs4601817 11 5268977 Intergenic G A 0.49 2.25 1.8E-06 1.4E-03 <.0001 -0.07 .05 0.17 .06
bg7 * 11 5270798 Intergenic G A 0.46 0.40 2.4E-07 1.8E-04 <.0001 0.05 .04 0.26 .06
rs7933082 11 5273186 Intergenic C G 0.48 0.47 1.5E-05 1.2E-02 0.0002 0.05 .04 0.36 .05
rs3888708 11 5274839 Intergenic T G 0.50 1.98 5.9E-05 4.5E-02 0.0009 -0.03 .04 0.47 .05
rs6578598 11 5275670 Intergenic T C 0.48 0.47 1.1E-05 8.4E-03 0.0002 0.04 .05 0.41 .05
rs10837774 11 5279964 OR51B4 A G 0.45 0.38 7.3E-08 5.5E-05 <.0001 0.05 .04 0.32 .04
rs3886223 11 5300323 OR51B2 T G 0.42 0.33 3.7E-11 ± 2.8E-08 <.0001 -0.01 .04 0.83 .04
rs2030090 11 5430669 OR51I2 G A 0.22 1.81 1.5E-03 1 0.01 0.04 .05 0.46 .04
rs449937 11 5446921 OR51A10P C T 0.16 2.08 5.2E-04 ± 3.9E-01 0.01 -0.03 .05 0.64 .03
rs366257 11 5447119 OR51A10P G A 0.16 2.21 2.3E-04 ± 1.7E-01 0.003 -0.03 .04 0.58 .03
rs446541 11 5448876 OR51A10P A T 0.26 0.48 2.5E-05 1.9E-02 0.0004 0.002 .07 0.96 .03
rs678343 11 64728207 CAPN1 G C 0.37 1.63 7.1E-04 ± 5.3E-01 0.01 0.04 .04 0.26 .03
rs593753 11 72369088 FCHSD2 T C 0.29 0.60 6.5E-04 ± 4.9E-01 0.01 0.05 .04 0.21 .02
rs638135 11 85863336 ME3 A G 0.23 0.59 1.1E-03 ± 8.3E-01 0.01 0.04 .06 0.32 .02
rs632538 11 85869341 ME3 G A 0.25 0.60 1.5E-03 ± 1 0.01 0.04 .06 0.35 .02
rs2580874 12 8650077 AICDA G A 0.20 0.54 4.5E-04 3.4E-01 0.01 0.09 .05 0.04 .02
rs1045411 13 29931232 HMGB1 A G 0.29 0.58 3.9E-04 2.9E-01 0.005 0.02 .05 0.70 .01
rs886599 14 70244197 Intergenic A G 0.10 2.70 1.2E-04 9.0E-02 0.002 0.04 .08 0.64 .01
rs1160027 17 51173101 Intergenic T G 0.20 0.56 8.5E-04 6.4E-01 0.01 -0.01 .06 0.79 .01
rs953695 18 59541550 SERPINB11 T G 0.21 1.83 7.6E-04 5.8E-01 0.01 -0.03 .04 0.63 .01
rs243341 19 4356106 CHAF1A T C 0.41 1.59 1.5E-03 1 0.01 -0.04 .04 0.33 .00
rs379327 19 61061978 NLRP4 A G 0.15 1.97 7.8E-04 5.9E-01 0.01 -0.07 .04 0.26 .00
rs639763 20 33325318 MMP24 T C 0.30 0.57 3.9E-04 2.9E-01 0.005 -0.04 .07 0.35 .00
rs6625978 X 71201690 PIN4 C A 0.06 3.35 1.3E-03 1 0.01 -0.001 .04 1.00 .00
  1. BP = location of SNP in base pairs in NCBI build 36
  2. Min = Minor allele
  3. Maj = Major allele
  4. Beta = Absolute change in HbF% on the log scale per copy of the minor allele
  5. SE = Standard error of the Beta estimate
  6. Bonf = Bonferroni adjusted P --value
  7. FDR = false discovery rate
  8. MAF = minor allele frequency
  9. * = SNP not in NCBI database
  10. ± = Chromosome 11 SNPs associated with disease severity at P < 0.05 after adjustment for Xmn1
  11. SNPs significantly associated with disease severity after Bonferroni correction are in bold
  12. P-values for SNPs associated with HbF% at P ≤ 0.05 in the mild disease group are in bold
  13. SNPs in italics were previously shown to be associated with disease severity in this sample by Ma et al. 2007 [19]
  14. Var = Percent of the variation in log transformed HbF% explained by each SNP