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. 2024 Dec 9;30(12):3614–3623. doi: 10.1038/s41591-024-03284-0

Table 1.

Genome-wide significant loci for multi-adiposity-adjusted PDFF and liver iron corrected T1 in the UK Biobank

Trait CHR POS Variant ID n Consequence A1 A2 A1Freq β s.e.m. P locus MAGMA
PDFF (WFM) 1 110232983 rs140584594 34,367 missense_variant A G 0.267 −0.049 0.007 1.42 × 10−13 GSTM1
PDFF (BMI) 1 172323134 rs17277932 35,146 intron_variant A G 0.145 0.049 0.008 5.91 × 10−9 DNM3
PDFF (VAT) 1 220970028 rs2642438 33,540 missense_variant A G 0.296 −0.061 0.006 7.89 × 10−24 MARC1 5.91 × 10−14
PDFF (BMI) 2 27730940 rs1260326 35,146 missense_variant T C 0.392 0.063 0.006 4.23 × 10−25 GCKR 4.51 × 10−14
PDFF (WFM) 2 165501927 rs5835988 34,367 intergenic_variant TG T 0.408 −0.046 0.006 3.25 × 10−14 COBLL1 3.58 × 10−11
PDFF (WFM) 2 227100579 2:227100579_TC_T 34,367 intergenic_variant TC T 0.348 −0.042 0.006 1.63 × 10−11 IRS1
PDFF (WFM) 3 12393125 rs1801282 34,367 missense_variant G C 0.122 −0.059 0.009 6.61 × 10−11 PPARG
PDFF (WFM) 3 25484121 rs79905393 34,367 intron_variant A G 0.036 −0.094 0.016 2.86 × 10−9 RARB
PDFF (WFM) 3 150066540 rs62271373 34,367 regulatory_region_variant A T 0.060 0.082 0.013 1.02 × 10−10 TSC22D2
PDFF (NA) 4 100239319 rs1229984 36,394 missense_variant T C 0.024 −0.165 0.023 1.26 × 10−12 ADH1B
PDFF (VAT) 4 100503761 rs11937107 33,540 intron_variant T C 0.252 −0.044 0.006 4.87 × 10−12 MTTP 8.20 × 10−12
PDFF (BMI) 4 100562374 rs36029295 35,146 intron_variant GA G 0.039 0.085 0.015 2.68 × 10−8 RP11-766F14.2
PDFF (VAT) 5 55808342 rs392794 33,540 intron_variant C T 0.254 −0.063 0.006 5.09 × 10−23 AC022431.2 6.83 × 10−13
PDFF (BMI) 5 72951153 5:72951153_GT_G 35,146 intron_variant G GT 0.462 0.033 0.006 3.45 × 10−8 ARHGEF28
PDFF (BMI) 6 26093141 rs1800562 35,146 missense_variant A G 0.077 0.062 0.011 3.27 × 10−8 HFE
PDFF (BMI) 7 28172732 rs702814 35,146 intron_variant C T 0.492 0.035 0.006 3.73 × 10−9 JAZF1
PDFF (VAT) 7 65431686 rs6955582 33,540 intron_variant A G 0.451 −0.034 0.006 1.72 × 10−9 GUSB 1.03 × 10−8
PDFF (VAT) 8 25464670 rs73221948 33,540 intergenic_variant T G 0.294 0.046 0.006 3.05 × 10−13 CDCA2
PDFF (BMI) 8 126500031 rs28601761 35,146 intron_variant G C 0.420 −0.072 0.006 1.63 × 10−32 TRIB1 4.72 × 10−7
PDFF (VAT) 9 132566666 rs7029757 33,540 non_coding_transcript_exon_variant A G 0.096 −0.063 0.009 3.15 × 10−11 TOR1B
PDFF (VAT) 10 113910721 rs1129555 33,540 3_prime_UTR_variant A G 0.273 0.062 0.006 2.52 × 10−23 GPAM 4.04 × 10−14
PDFF (VAT) 10 114024573 10:114024573_GA_G 33,540 intergenic_variant G GA 0.286 −0.039 0.006 2.24 × 10−10 TECTB 4.90 × 10−9
PDFF (WFM) 11 823586 rs140201358 34,367 missense_variant G C 0.015 0.147 0.025 2.35 × 10−9 PNPLA2
PDFF (VAT) 11 75456134 rs531117 33,540 downstream_gene_variant T C 0.157 −0.042 0.008 3.91 × 10−8 MOGAT2
PDFF (NA) 12 3685100 rs1985912 36,394 intron_variant G A 0.326 −0.043 0.008 2.67 × 10−8 PRMT8
PDFF (WFM) 12 124476873 rs12833624 34,367 intron_variant T C 0.337 −0.039 0.006 3.37 × 10−10 FAM101A 1.01 × 10−6
PDFF (VAT) 17 7116853 rs446994 33,540 intron_variant C A 0.422 0.033 0.006 3.43 × 10−9 DLG4 1.04 × 10−8
PDFF (NA) 17 17974014 rs11439486 36,394 downstream_gene_variant T TA 0.330 0.046 0.008 7.63 × 10−9 GID4 2.19 × 10−7
PDFF (VAT) 17 64210580 rs1801689 33,540 missense_variant C A 0.029 0.099 0.016 1.63 × 10−9 APOH
PDFF (NA) 19 18229208 rs56252442 36,394 intron_variant T G 0.253 0.048 0.008 5.11 × 10−9 MAST3 5.13 × 10−7
PDFF (VAT) 19 19379549 rs58542926 33,540 missense_variant T C 0.075 0.292 0.011 4.7 × 10−168 TM6SF2 5.00 × 10−10
PDFF (VAT) 19 33834096 rs73026242 33,540 downstream_gene_variant G A 0.072 0.060 0.011 3.59 × 10−8 CEBPG
PDFF (BMI) 19 45411941 rs429358 35,146 missense_variant C T 0.151 −0.102 0.008 2.92 × 10−35 APOE 1.67 × 10−15
PDFF (NA) 19 45830763 rs344790 36,394 upstream_gene_variant A C 0.421 0.043 0.007 2.68 × 10−9 CKM
PDFF (VAT) 19 54671421 rs60204587 33,540 intron_variant A G 0.426 0.045 0.006 1.42 × 10−15 MBOAT7 5.27 × 10−15
PDFF (WFM) 20 39142516 rs2207132 34,367 intergenic_variant A G 0.034 0.092 0.016 1.73 × 10−8 MAFB
PDFF (VAT) 22 44324730 rs738408 33,540 synonymous_variant T C 0.214 0.237 0.007 1.7 × 10−269 PNPLA3 1.38 × 10−14
cT1 (BMI) 1 15810346 rs12130283 29,312 intron_variant C T 0.484 0.045 0.007 5.33 × 10−10 CELA2B 6.91 × 10−8
cT1 (BMI) 1 220100497 rs759359281 29,312 splice_polypyrimidine_tract_variant C CA 0.055 0.129 0.016 4.74 × 10−15 SLC30A10
cT1 (VAT) 4 103188709 rs13107325 27,782 missense_variant T C 0.070 0.556 0.015 <4.94 × 10−324 SLC39A8 2.01 × 10−18
cT1 (VAT) 6 25878848 rs55925606 27,782 intron_variant G A 0.073 −0.149 0.015 1.07 × 10−24 SLC17A3 3.32 × 10−9
cT1 (VAT) 8 9173209 rs7012637 27,782 intron_variant A G 0.472 0.043 0.007 9.39 × 10−9 RP11-10A14.4
cT1 (BMI) 8 18272881 rs1495741 29,312 regulatory_region_variant G A 0.219 −0.064 0.009 4.5 × 10−13 NAT2
cT1 (NA) 9 136149830 rs532436 30,481 intron_variant A G 0.183 0.079 0.010 7.47 × 10−15 ABO
cT1 (WFM) 10 113921825 rs2792735 28,638 intron_variant G A 0.277 0.046 0.008 4.05 × 10−8 GPAM 4.81 × 10−7
cT1 VAT) 11 61549025 rs174533 27,782 intron_variant A G 0.351 0.052 0.008 2.49 × 10−11 MYRF 3.51 × 10−7
cT1 (NA) 12 51511269 rs59372312 30,481 intron_variant G A 0.067 −0.088 0.016 2.33 × 10−8 TFCP2
cT1 (BMI) 14 24572932 rs111723834 29,312 missense_variant A G 0.016 0.383 0.029 1.7 × 10−39 PCK2 9.99 × 10−8
cT1 (VAT) 16 77423427 rs2454933 27,782 intron_variant T C 0.082 0.075 0.014 3.69 × 10−8 ADAMTS18
cT1 (NA) 18 59323966 18:59323966_CTT_C 30,481 intron_variant C CTT 0.287 −0.050 0.009 1.28 × 10−8 CDH20
cT1 (WFM) 19 19379549 rs58542926 28,638 missense_variant T C 0.074 0.141 0.014 4.22 × 10−23 TM6SF2 4.46 × 10−7
cT1 (VAT) 19 33890838 rs10406327 27,782 intron_variant G C 0.477 −0.042 0.007 1.24 × 10−8 PEPD 1.84 × 10−06
cT1 (BMI) 19 49206172 rs516246 29,312 intron_variant C T 0.489 −0.053 0.007 3.67 × 10−13 FUT2 1.00 × 10−13
cT1 (VAT) 22 37469192 rs6000553 27,782 intron_variant A G 0.466 0.070 0.007 7.53 × 10−21 TMPRSS6 4.81 × 10−12
cT1 (BMI) 22 44324727 rs738409 29,312 missense_variant G C 0.214 0.120 0.009 3.2 × 10−41 PNPLA3 2.85 × 10−13

The association between common genetic variants and PDFF under different adiposity adjustments was performed using REGENIE adjusting for adiposity index, age, sex, age × sex, age2 and age2 × sex, first ten genomic principal components and array batch. Each adiposity adjustment is shown in parentheses. Genomic loci in bold represent the previously unknown loci identified in the present work. The locus column shows the nearest gene to the lead variant (from COJO analysis) at each locus. MAGMA column shows significant gene-based associations at each locus exceeding Bonferroni threshold (P < 2.65 × 10−6). Sample size used in each GWAS has been shown in column N. P values were not corrected for multiple testing among four different models (unadjusted, adjusted for BMI, WFM and VAT). NA, unadjusted; MAGMA, multi-marker analysis of genomic annotation.