Table 1

List of replicated genetic loci in which all SNPs have P < 5E−5 for both circulating LDL-C and T2D and with opposite directions of effect, for UK Biobank LDL-C and DIAGRAM T2D

UK Biobank LDL-C and DIAGRAM T2DGLGC
Chrbp_minbp_maxNearest genesTop SNP-metaCCAmetaCCA-min PT2D βT2D PLDL βLDL PTop SNP-metaCCALDL PmetaCCA P
1109,285,825109,285,825FNDC7-STXBP3rs121446586.7E−10−0.0958.3E−060.0287.0E−06rs121446581.7E−034.2E−07
1109,843,746110,078,255SORT1-PSMA5rs562185862.0E−178−0.0598.1E−060.0952.6E−118rs176475436.3E−272.5E−32
227,161,47628,246,841GCKRrs65476921.4E−194−0.0551.6E−170.0438.1E−113rs12603268.4E−101.3E−32
243,452,18344,020,441THADArs1160970552.2E−150.181.5E−10−0.0341.7E−06rs558778051.1E−032.4E−29
2121,306,440121,350,667LINC01101-GLI2rs170502722.0E−51−0.0313.5E−060.0266.4E−42rs8964998.9E−094.7E−12
2234,508,963234,565,917UGT1A8rs27410388.5E−09−0.031.5E−050.0093.8E−05rs27410193.5E−062.5E−09
312,058,24612,456,689PPARGrs170361701.8E−19−0.132.7E−060.0739.9E−15rs170363261.5E−081.2E−24
3124,912,207129,301,874SLC12A8rs98735191.8E−16−0.0391.4E−090.0111.9E−08rs46793703.2E−042.7E−10
3170,631,635170,743,747SLC2A2rs124967348.0E−180.052.5E−07−0.0204.5E−12rs74306724.2E−051.1E−15
574,352,18075,042,913HMGCR-POC5rs343616.9E−322−0.058.7E−140.0543.3E−156rs77030513.0E−867.5E−118
578,350,39078,385,845BHMT2rs5920521.7E−100.0311.1E−06−0.0081.3E−05rs5573023.0E−032.3E−07
631,145,92031,372,569HLA-C/Brs360577351.4E−15−0.0376.7E−060.0162.3E−11rs77437612.5E−112.5E−10
632,127,47733,514,567HLA-DQA1/B1rs31302761.8E−100.0313.8E−06−0.0094.4E−06rs92752213.6E−151.0E−23
6126,629,425127,167,072CENPWrs93884903.2E−29−0.0494.5E−140.0153.2E−15rs93884903.8E−038.9E−15
744,585,05244,709,372NPC1L1-DDX56rs20084282.9E−780.0314.8E−05−0.0384.5E−63rs2173866.3E−224.3E−23
7100,266,081100,414,386GIGYF1-POP7-EPOrs2217932.5E−24−0.0471.9E−050.0296.7E−20rs5065974.8E−043.5E−08
89,168,1469,740,317PPP1R3Brs99872891.6E−880.0663.9E−09−0.0571.1E−65rs99872891.4E−271.4E−36
1064,988,93165,340,897REEP3rs38473268.4E−15−0.0281.3E−050.0129.2E−11rs127752311.1E−036.7E−06
10101,900,579102,039,463ERLIN1-CWF19L1rs356147922.8E−150.0311.9E−06−0.0122.2E−10rs3691365331.8E−038.5E−08
1165,422,85365,604,195OVOL1-SNX32rs343810091.2E−090.0372.3E−05−0.0122.8E−06rs38147074.3E−046.5E−08
1250,881,14850,987,378DIP2Brs73168643.3E−11−0.0294.6E−050.0116.7E−08rs108760411.1E−061.2E−06
12121,435,778123,891,209HNF1A-OASLrs122318068.5E−17−0.058.0E−080.0181.4E−10rs71316964.4E−061.4E−15
1562,383,15563,314,519C2CD4A/Brs18814152.8E−170.0474.7E−13−0.0081.8E−05rs45021561.1E−045.0E−14
1729,628,54929,749,444NF1-EVI2Ars75025569.7E−190.0325.3E−07−0.0142.8E−13rs11295065.8E−069.2E−08
1746,044,03146,114,620COPZ2rs129358903.0E−17−0.0326.6E−060.0156.2E−13rs116512753.6E−032.4E−07
1919,320,82519,793,545TM6SF2rs591487999.9E−324−0.0543.4E−080.0771.4E−162rs104019694.6E−611.6E−86
1945,324,75645,428,234APOErs101194.9E−420.0433.5E−09−0.0243.1E−31rs20756500.0E+000.0E+00
1946,123,92946,314,504GIPRrs22386892.0E−33−0.051.3E−140.0179.4E−19rs104226011.9E−093.4E−22
2042,958,76843,042,364HNF4Ars18009615.3E−72−0.163.2E−200.0761.8E−42rs18009615.2E−117.1E−31
2218,415,15818,486,514MICAL3rs59929283.6E−110.0353.1E−06−0.0117.9E−07rs72866073.4E−052.4E−08
2244,324,73044,394,402PNPLA3rs7384084.6E−19−0.0491.8E−100.0147.1E−10rs7384082.9E−051.9E−11
  • β-Coefficients refer to the SNP with the lowest P value for each trait in the respective region. The minimum univariate P value for LDL-C in GLGC summary statistics as well as the top SNP and P value of the top metaCCA SNP for the region discovered in UK Biobank is also shown. bp_min and bp_max are the minimum and maximum base pair position for which all SNPs have P < 5E−5 for LDL-C and T2D, with opposite directions of effect, and with metaCCA P < 5E−8. Human build GRCh37/hg19; β-coefficients correspond to log-ORs for T2D and SDs for LDL-C. P values from GLGC LDL-C associations are for SNPs showing opposite direction of association with T2D (DIAGRAM). Chr, chromosome.