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.