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. 2014 Mar 6;10(3):e1004160. doi: 10.1371/journal.pgen.1004160

Table 3. Candidate genes and intergenic SNPs for T2D and obesity that exhibit differential DNA methylation in human pancreatic islets of 34 non-diabetic compared with 15 T2D donors.

Gene symbol Probe ID Non-diabetic DNA methylation (%) T2D DNA methylation (%) Delta DNA methylation (%) P-value q-value Chr. Position Gene region GWAS trait
ADAMTS9 cg25859972 41.19±5.74 34.53±6.83 −6.66 1.2×10−3 0.047 3 64645555 Body T2D
ADCY5 cg27182923 61.63±6.82 56.96±5.94 −4.67 5.3×10−4 0.037 3 124612077 Body T2D
ADCY5 cg01246398 58.41±6.73 52.33±6.35 −6.08 5.6×10−4 0.037 3 124648562 Body T2D
ADCY5 cg25976932 61.85±7.04 55.45±7.33 −6.40 6.6×10−4 0.037 3 124621648 Body T2D
ADCY5 cg02953559 71.50±6.41 64.82±6.40 −6.68 8.6×10−4 0.041 3 124647654 Body T2D
ADCY5 cg15464481 62.27±9.16 53.27±8.45 −9.01 3.5×10−4 0.037 3 124634652 Body T2D
BCL11A cg03606511 69.40±5.07 64.87±5.81 −4.52 1.4×10−3 0.049 2 60589034 Body T2D
CDKAL1 cg12556823 85.75±2.64 85.30±3.64 −0.45 7.3×10−4 0.039 6 21131464 Body T2D
DUSP8 cg14488974 71.10±3.93 67.35±3.70 −3.75 4.1×10−5 0.016 11 1536002 Body T2D
FTO cg26982104 29.73±5.52 23.13±4.72 −6.60 3.6×10−4 0.037 16 52336836 Body T2D and obesity
FTO cg01485549 64.84±9.62 56.14±10.53 −8.70 5.2×10−4 0.037 16 52346986 Body T2D and obesity
HHEX cg20180364 61.64±4.26 58.49±4.91 −3.15 1.4×10−3 0.049 10 94438512 TSS1500 T2D
HHEX cg09721427 30.62±4.09 27.26±3.75 −3.36 7.2×10−4 0.039 10 94438682 TSS1500 T2D
HHEX cg16508068 55.98±5.16 51.97±4.77 −4.01 8.5×10−4 0.041 10 94441716 Body T2D
HHEX cg26979504 44.33±4.65 38.62±5.44 −5.71 2.6×10−4 0.033 10 94441498 Body T2D
HMGA2 cg03257822 10.29±1.49 9.09±0.92 −1.20 5.1×10−4 0.037 12 64503074 TSS1500;Body T2D
HNF1B cg21250756 28.57±5.12 20.71±3.83 −7.86 5.2×10−6 0.004 17 33151413 Body T2D
IGF2BP2 cg21531679 66.37±3.80 64.27±4.44 −2.10 1.4×10−3 0.049 3 186937720 Body T2D
IRS1 cg04751089 40.02±6.28 33.09±4.40 −6.93 5.5×10−5 0.016 2 227367880 3′UTR T2D
IRS1 cg05263838 41.54±8.39 34.27±4.43 −7.27 1.1×10−3 0.047 2 227367650 3′UTR T2D
JAZF1 cg23597162 80.20±3.06 77.41±4.33 −2.79 6.1×10−5 0.016 7 28068866 Body T2D
JAZF1 cg14491535 72.77±4.13 68.59±3.00 −4.18 5.0×10−4 0.037 7 28161615 Body T2D
JAZF1 cg11526778 57.89±5.31 52.87±5.74 −5.02 6.0×10−4 0.037 7 28082308 Body T2D
KCNQ1 cg08895013 72.11±3.47 68.49±3.95 −3.62 1.2×10−4 0.022 11 2424908 Body T2D
KCNQ1 cg20533553 51.83±4.37 47.76±4.90 −4.08 6.3×10−4 0.037 11 2421398 TSS1500 T2D
KCNQ1 cg26896748 87.66±4.31 83.55±6.85 −4.11 5.5×10−4 0.037 11 2817640 Body T2D
KCNQ1 cg17305275 81.71±2.92 77.27±4.61 −4.44 1.1×10−3 0.047 11 2703251 Body T2D
KCNQ1 cg03371125 53.56±5.40 48.66±5.26 −4.89 6.2×10−4 0.037 11 2421421 TSS1500 T2D
KCNQ1 cg03600094 69.15±6.30 63.30±5.93 −5.85 1.5×10−4 0.023 11 2438051 TSS1500;Body T2D
KCNQ1 cg01693193 72.51±5.35 66.36±5.69 −6.15 4.6×10−5 0.016 11 2661729 Body T2D
KCNQ1 cg03170016 65.77±8.65 56.41±8.93 −9.36 2.6×10−4 0.033 11 2438718 TSS1500;Body T2D
PPARG cg04908300 37.30±3.34 34.33±3.41 −2.98 1.3×10−4 0.022 3 12305532 5′UTR;1stExon T2D
PPARG cg10499651 64.69±7.28 59.92±7.95 −4.77 1.4×10−3 0.049 3 12440415 Body T2D
RBMS1 cg01757209 4.43±0.61 4.18±0.63 −0.26 1.3×10−3 0.047 2 160972619 Body T2D
TCF7L2 cg26380291 64.60±4.36 60.94±4.43 −3.67 9.8×10−4 0.045 10 114777833 Body T2D
TCF7L2 cg07591090 78.39±5.70 72.44±5.97 −5.95 1.1×10−3 0.047 10 114867606 Body T2D
TCF7L2 cg06403317 72.53±6.12 65.26±7.39 −7.26 1.5×10−3 0.049 10 114867642 Body T2D
TCF7L2 cg03384318 78.28±6.67 70.43±7.19 −7.85 4.4×10−4 0.037 10 114867679 Body T2D
TCF7L2 cg03510732 56.92±8.96 47.90±8.59 −9.02 1.3×10−3 0.047 10 114861921 Body T2D
THADA cg22076676 41.57±3.33 38.39±3.06 −3.18 1.2×10−3 0.047 2 43357439 Body T2D
THADA cg24168549 80.90±4.90 75.99±4.62 −4.91 1.3×10−4 0.022 2 43507634 Body T2D
THADA cg19211851 45.34±6.67 39.76±6.96 −5.58 7.9×10−4 0.040 2 43408970 Body T2D
THADA cg01649611 70.96±4.93 63.16±5.91 −7.81 5.4×10−8 0.003 2 43374570 Body T2D
rs5015480 cg20134984 77.88±3.57 74.62±5.58 −3.26 6.0×10−4 0.037 10 94446626 intergenic T2D
FAIM2 cg04920032 19.84±3.59 15.68±3.01 −4.16 1.4×10−5 0.010 12 48549253 3′UTR Obesity
NPC1 cg21243631 61.24±4.09 56.37±4.38 −4.87 1.0×10−6 0.001 18 19408258 Body Obesity
VEGFA cg01298514 80.65±3.69 74.63±4.99 −5.72 3.7×10−5 0.018 6 43844785 TSS1500 Obesity

Probes shown in bold are CpG sites with an absolute difference in DNA methylation >5% between non-diabetic and T2D human islets. q-values are based on a FDR analysis.