Table 1.

Lipid-Associated CpG Sites Replicated in Independent Cohorts With Whole Blood or CD4+ T Cells DNA Methylation

Lipid TraitType of LociCpGChrPositionGene PropertyGeneDirection*Discovery β (SE)P ValueDirectionReplication β (SE)P Value
Primary model
TCNovelcg17901584155353706TSS1500DHCR24++0.000149 (0.000027)4.73E-08+++0.000114 (0.000032)3.80E-04
TCNovelcg23759710242990957First exonOXER1−−−0.000082 (0.000014)2.45E-09−−+−0.000074 (0.000022)8.32E-04
TCNovelcg002853948126011954BodySQLE++0.000213 (0.000034)5.98E-10+++0.000161 (0.000039)3.16E-05
TCNovelcg078394571657023022TSS1500NLRC5++0.000273 (0.000051)8.74E-08+++0.000231 (0.000049)2.32E-06
TCNovelcg099780772242229983BodySREBF2++0.000057 (0.000010)1.79E-09+++0.000047 (0.000014)4.82E-04
LDL-CNovelcg002853948126011954BodySQLE++0.000230 (0.000039)4.12E-09++0.000200 (0.000045)1.04E-05
HDL-CNovelcg17901584155353706TSS1500DHCR24++0.000717 (0.000052)5.47E-43++0.000321 (0.000090)3.55E-04
HDL-CNovelcg0756772411537777213′UTRGATAD2B−−−0.000248 (0.000045)3.81E-08−−−0.000311 (0.000087)3.53E-04
HDL-CNovelcg1935116622091336325′UTRPIKFYVE−−−0.000207 (0.000038)4.16E-08−−−0.000279 (0.000065)1.96E-05
HDL-CNovelcg06560379644231305BodyNFKBIE++0.000114 (0.000017)6.05E-11++0.000083 (0.000023)2.76E-04
HDL-CNovelcg164076991074020428−−−0.000280 (0.000048)7.30E-09−−−0.000265 (0.000069)1.09E-04
HDL-CNovelcg1975065713389359673′UTRUFM1−−−0.000308 (0.000049)2.24E-10−−−0.000329 (0.000063)2.20E-07
HDL-CNovelcg078143181531624584BodyKLF13−−−0.000322 (0.000049)6.38E-11−−−0.000455 (0.000121)1.69E-04
HDL-CNovelcg061928831552554171BodyMYO5C−−−0.000258 (0.000043)2.04E-09−−−0.000283 (0.000053)8.95E-08
HDL-CNovelcg110246821717730094BodySREBF1−−−0.000213 (0.000036)4.19E-09−−−0.000229 (0.000058)8.72E-05
HDL-CPreviouscg065001612143656587BodyABCG1−−−0.000459 (0.000037)1.20E-34−−−0.000322 (0.000072)7.43E-06
HDL-CNovelcg0639716122397600595′UTR/BodySPRY4−−−0.000259 (0.000048)7.25E-08−−−0.000327 (0.000075)1.27E-05
TGNovelcg037253091109757585BodySARS−−−0.009052 (0.001209)7.11E-14−−−−0.011098 (0.001746)2.09E-10
TGNovelcg162465451120255941BodyPHGDH−−−0.012602 (0.002184)7.94E-09−−−−0.007394 (0.002158)6.11E-04
TGNovelcg144761011120255992BodyPHGDH−−−0.021504 (0.002789)1.25E-14−−−−0.012696 (0.002473)2.82E-07
TGPreviouscg1969303111454415523′UTRTXNIP−−−0.017424 (0.002249)9.40E-15−−−−0.010932 (0.002263)1.35E-06
TGNovelcg066905484139162808BodySLC7A11−−−0.021855 (0.002394)6.98E-20−−−−0.007707 (0.001666)3.70E-06
TGNovelcg21429551730635762BodyGARS−−−0.026953 (0.003214)4.97E-17−−−−0.012744 (0.002780)4.57E-06
TGNovelcg03068497730635838BodyGARS−−−0.025125 (0.003427)2.27E-13−−−−0.012680 (0.002935)1.55E-05
TGNovelcg19390658730636176BodyGARS−−−0.020977 (0.002685)5.61E-15−−−−0.012653 (0.002450)2.40E-07
TGPreviouscg0750497710102131012++0.012564 (0.002025)5.45E-10+++0.011962 (0.001901)3.10E-10
TGPreviouscg0057495811686076225′UTRCPT1A−−−0.008999 (0.000724)1.65E-35−+−−0.011979 (0.001126)2.01E-26
TGPreviouscg0973719711686076755′UTRCPT1A−−−0.007154 (0.001104)9.13E-11−+−−0.010376 (0.001785)6.18E-09
TGPreviouscg1705847511686077375′UTRCPT1A−−−0.009858 (0.001003)8.33E-23−−−−0.013425 (0.001665)7.55E-16
TGNovelcg081290171717728660BodySREBF1++0.009755 (0.001627)2.02E-09+++0.011616 (0.002263)2.84E-07
TGPreviouscg110246821717730094BodySREBF1++0.010107 (0.001327)2.59E-14+++0.010284 (0.001345)2.07E-14
TGNovelcg088577971740927699BodyVPS25++0.009577 (0.001708)2.06E-08+++0.007994 (0.001849)1.53E-05
TGNovelcg0271160819472879645′UTR/BodySLC1A5−−−0.008321 (0.001310)2.14E-10−−−−0.004606 (0.001200)1.24E-04
TGPreviouscg2724368521436423665′UTR/BodyABCG1++0.012223 (0.001164)8.12E-26+++0.004508 (0.001093)3.72E-05
TGNovelcg011760282143653234BodyABCG1++0.006953 (0.001189)5.00E-09+++0.011307 (0.002056)3.82E-08
TGPreviouscg065001612143656587BodyABCG1++0.019854 (0.001359)2.29E-48+++0.012731 (0.001637)7.55E-15
Secondary BMI-adjusted model
TCNovelcg23759710242990957First exonOXER1−−−0.000081 (0.000014)3.60E-09−−−−0.000075 (0.000022)7.75E-04
TCNovelcg002853948126011954BodySQLE++0.000215 (0.000035)4.83E-10+++0.000155 (0.000039)6.08E-05
TCNovelcg078394571657023022TSS1500NLRC5++0.000272 (0.000051)9.62E-08+++0.000223 (0.000049)5.54E-06
TCNovelcg099780772242229983BodySREBF2++0.000057 (0.000010)3.03E-09+++0.000047 (0.000014)6.52E-04
LDL-CNovelcg002853948126011954BodySQLE++0.000234 (0.000039)2.32E-09++0.000197 (0.000046)1.82E-05
HDL-CNovelcg19273683121656047BodyECE1−−−0.000289 (0.000051)1.50E-08−−−0.000244 (0.000078)1.71E-03
HDL-CPreviouscg065001612143656587BodyABCG1−−−0.000363 (0.000039)2.48E-20−−−0.000219 (0.000075)3.41E-03
TGNovelcg037253091109757585BodySARS−−−0.007844 (0.001258)4.56E-10−−−−0.009679 (0.001832)1.27E-07
TGNovelcg144761011120255992BodyPHGDH−−−0.018779 (0.002897)8.96E-11−−−−0.009380 (0.002574)2.68E-04
TGPreviouscg1969303111454415523′UTRTXNIP−−−0.016514 (0.002340)1.70E-12−−−−0.010270 (0.002376)1.54E-05
TGNovelcg066905484139162808BodySLC7A11−−−0.019833 (0.002487)1.54E-15−−−−0.006180 (0.001744)3.95E-04
TGNovelcg21429551730635762BodyGARS−−−0.023803 (0.003349)1.18E-12−−−−0.009124 (0.002903)1.67E-03
TGNovelcg19390658730636176BodyGARS−−−0.020864 (0.002797)8.73E-14−−−−0.010873 (0.002568)2.30E-05
TGPreviouscg0057495811686076225′UTRCPT1A−−−0.007903 (0.000750)5.81E-26−+−−0.010401 (0.001177)9.59E-19
TGPreviouscg0973719711686076755′UTRCPT1A−−−0.007034 (0.001152)1.01E-09−+−−0.010243 (0.001874)4.58E-08
TGPreviouscg1705847511686077375′UTRCPT1A−−−0.009144 (0.001046)2.24E-18−−−−0.012478 (0.001746)8.93E-13
TGNovelcg081290171717728660BodySREBF1++0.009346 (0.001693)3.36E-08+++0.010037 (0.002373)2.85E-05
TGPreviouscg2724368521436423665′UTR/BodyABCG1++0.010416 (0.001204)5.08E-18+++0.004038 (0.001146)4.26E-04
TGPreviouscg065001612143656587BodyABCG1++0.016873 (0.001396)1.29E-33+++0.010841 (0.001712)1.10E-06
  • BMI indicates body mass index; Chr, chromosome; CpG, cytosine–guanine dinucleotide; HDL-C, high-density lipoprotein cholesterol; LDL-C, low-density lipoprotein cholesterol; TC, total cholesterol; and TG, triglyceride.

  • * Direction of effect in Framingham Heart Study and Prospective Investigation of the Vasculature in Uppsala Seniors Study.

  • Direction of effect in LBC1936 (Lothian Birth Cohorts of 1936), LBC1921, and GOLDN (Genetics of Lipid Lowering Drugs and Diet Network) for TC and TG, and direction of effect in LBC1936 and GOLDN for LDL-C and HDL-C.