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CpG interval report generated on 20/05/20 with pycoMeth 0.4.6
Interval details
| pvalue rank | chromosome | start | end | length | number of samples | number of CpGs | pvalue | adjusted pvalue |
|---|---|---|---|---|---|---|---|---|
| #197 | 7 | 44962443 | 44963350 | 907 | 3 | 31 | 3.09966e-14 | 1.56478e-12 |
Methylation log-likelihood ratio by CpG position
Distribution of CpG methylation log-likelihood ratio by sample
Closest transcripts TSS
| distance to tss | transcript id | gene id | transcript name | chromosome | start | end | strand | feature type | transcript biotype |
|---|---|---|---|---|---|---|---|---|---|
| -1534 | enst00000568457 | sg00000260997 | ac004847.1-201 | 7 | 44958999 | 44960909 | - | lnc_RNA | lncrna |
| 11756 | enst00000488554 | sg00000136286 | myo1g-206 | 7 | 44962666 | 44975106 | - | lnc_RNA | retained_intron |
| 11865 | enst00000463516 | sg00000136286 | myo1g-202 | 7 | 44962666 | 44975215 | - | lnc_RNA | retained_intron |
| 15650 | enst00000480503 | sg00000136286 | myo1g-204 | 7 | 44968523 | 44979000 | - | lnc_RNA | retained_intron |
| 15665 | enst00000258787 | sg00000136286 | myo1g-201 | 7 | 44962662 | 44979015 | - | mRNA | protein_coding |
| 15683 | enst00000648014 | sg00000136286 | myo1g-208 | 7 | 44962856 | 44979033 | - | mRNA | protein_coding |
| 15719 | enst00000495831 | sg00000136286 | myo1g-207 | 7 | 44962662 | 44979069 | - | mRNA | nonsense_mediated_decay |
| 15729 | enst00000483585 | sg00000136286 | myo1g-205 | 7 | 44962662 | 44979079 | - | lnc_RNA | retained_intron |
| 15738 | enst00000464434 | sg00000136286 | myo1g-203 | 7 | 44968523 | 44979088 | - | mRNA | nonsense_mediated_decay |
| 22160 | enst00000384215 | sg00000277184 | snora9-201 | 7 | 44985378 | 44985510 | - | snoRNA | snorna |
| 23210 | enst00000584327 | sg00000232956 | snhg15-208 | 7 | 44983137 | 44986560 | - | lnc_RNA | lncrna |
| 23220 | enst00000438705 | sg00000232956 | snhg15-201 | 7 | 44983085 | 44986570 | - | lnc_RNA | lncrna |
| 23287 | enst00000577700 | sg00000232956 | snhg15-202 | 7 | 44983023 | 44986637 | - | lnc_RNA | lncrna |
| 23300 | enst00000580458 | sg00000232956 | snhg15-205 | 7 | 44983034 | 44986650 | - | lnc_RNA | lncrna |
| 23306 | enst00000579383 | sg00000232956 | snhg15-204 | 7 | 44983026 | 44986656 | - | lnc_RNA | lncrna |
| 23315 | enst00000653305 | sg00000232956 | snhg15-211 | 7 | 44983086 | 44986665 | - | lnc_RNA | lncrna |
| 23318 | enst00000667823 | sg00000232956 | snhg15-213 | 7 | 44983026 | 44986668 | - | lnc_RNA | lncrna |
| 23318 | enst00000584686 | sg00000232956 | snhg15-209 | 7 | 44983847 | 44986668 | - | lnc_RNA | lncrna |
| 23319 | enst00000585030 | sg00000232956 | snhg15-210 | 7 | 44983026 | 44986669 | - | lnc_RNA | lncrna |
| 23324 | enst00000582727 | sg00000232956 | snhg15-207 | 7 | 44983028 | 44986674 | - | lnc_RNA | lncrna |
| 23343 | enst00000667119 | sg00000232956 | snhg15-212 | 7 | 44983039 | 44986693 | - | lnc_RNA | lncrna |
| 23349 | enst00000668580 | sg00000232956 | snhg15-214 | 7 | 44983023 | 44986699 | - | lnc_RNA | lncrna |
| 23484 | enst00000578968 | sg00000232956 | snhg15-203 | 7 | 44983023 | 44986834 | - | lnc_RNA | lncrna |
| 23611 | enst00000580528 | sg00000232956 | snhg15-206 | 7 | 44983038 | 44986961 | - | lnc_RNA | lncrna |
| 36125 | enst00000461377 | sg00000136280 | ccm2-203 | 7 | 44999475 | 45076352 | + | lnc_RNA | processed_transcript |
| 36835 | enst00000258781 | sg00000136280 | ccm2-201 | 7 | 45000185 | 45076467 | + | mRNA | protein_coding |
| 36838 | enst00000541586 | sg00000136280 | ccm2-218 | 7 | 45000188 | 45076469 | + | mRNA | protein_coding |
| 36838 | enst00000544363 | sg00000136280 | ccm2-219 | 7 | 45000188 | 45076469 | + | mRNA | protein_coding |
| 36839 | enst00000478582 | sg00000136280 | ccm2-211 | 7 | 45000189 | 45073519 | + | lnc_RNA | processed_transcript |
| 36899 | enst00000488727 | sg00000136280 | ccm2-216 | 7 | 45000249 | 45076414 | + | mRNA | nonsense_mediated_decay |
| 36950 | enst00000648329 | sg00000136280 | ccm2-220 | 7 | 45000300 | 45076408 | + | mRNA | nonsense_mediated_decay |
| -42774 | enst00000440356 | sg00000230160 | ac004854.1-201 | 7 | 44919669 | 44920329 | + | pseudogenic_transcript | processed_pseudogene |
| 63665 | enst00000478169 | sg00000136280 | ccm2-210 | 7 | 45027015 | 45064494 | + | lnc_RNA | processed_transcript |
| 63676 | enst00000475551 | sg00000136280 | ccm2-207 | 7 | 45027026 | 45076451 | + | mRNA | protein_coding |
| 64284 | enst00000381112 | sg00000136280 | ccm2-202 | 7 | 45027634 | 45076469 | + | mRNA | protein_coding |
| 64322 | enst00000492883 | sg00000136280 | ccm2-217 | 7 | 45027672 | 45073166 | + | lnc_RNA | retained_intron |
| 64322 | enst00000480658 | sg00000136280 | ccm2-213 | 7 | 45027672 | 45073288 | + | lnc_RNA | retained_intron |
| 64322 | enst00000474617 | sg00000136280 | ccm2-206 | 7 | 45027672 | 45076431 | + | mRNA | protein_coding |
| 64322 | enst00000482714 | sg00000136280 | ccm2-215 | 7 | 45027672 | 45071180 | + | lnc_RNA | processed_transcript |
| 64351 | enst00000472223 | sg00000136280 | ccm2-205 | 7 | 45027701 | 45070557 | + | lnc_RNA | processed_transcript |
| 74911 | enst00000476594 | sg00000136280 | ccm2-208 | 7 | 45038261 | 45064622 | + | lnc_RNA | processed_transcript |
| -76913 | enst00000395699 | sg00000146676 | purb-201 | 7 | 44876299 | 44885530 | - | mRNA | protein_coding |
| -77490 | enst00000608450 | sg00000272768 | ac004854.2-201 | 7 | 44884953 | 44886393 | + | lnc_RNA | lncrna |
| -80643 | enst00000578157 | sg00000284261 | mir4657-201 | 7 | 44881748 | 44881800 | - | miRNA | mirna |
| 101253 | enst00000481194 | sg00000136280 | ccm2-214 | 7 | 45064603 | 45076453 | + | lnc_RNA | retained_intron |
| 104286 | enst00000477605 | sg00000136280 | ccm2-209 | 7 | 45067636 | 45076437 | + | lnc_RNA | retained_intron |
| 105144 | enst00000480382 | sg00000136280 | ccm2-212 | 7 | 45068494 | 45072786 | + | mRNA | protein_coding |
| 108988 | enst00000470837 | sg00000136280 | ccm2-204 | 7 | 45072338 | 45073562 | + | lnc_RNA | retained_intron |
| -113384 | enst00000450016 | sg00000234183 | linc01952-202 | 7 | 44849059 | 44849565 | + | lnc_RNA | lncrna |
| -114027 | enst00000443162 | sg00000234183 | linc01952-201 | 7 | 44848416 | 44849568 | + | lnc_RNA | lncrna |
| -114360 | enst00000446531 | sg00000105968 | h2az2-207 | 7 | 44834925 | 44848083 | - | mRNA | protein_coding |
| -114361 | enst00000437072 | sg00000105968 | h2az2-206 | 7 | 44829897 | 44848082 | - | mRNA | protein_coding |
| -114363 | enst00000381124 | sg00000105968 | h2az2-205 | 7 | 44834239 | 44848080 | - | mRNA | protein_coding |
| -114366 | enst00000222690 | sg00000105968 | h2az2-201 | 7 | 44826791 | 44848077 | - | mRNA | protein_coding |
| -114367 | enst00000350771 | sg00000105968 | h2az2-204 | 7 | 44834228 | 44848076 | - | mRNA | protein_coding |
| -114380 | enst00000308153 | sg00000105968 | h2az2-202 | 7 | 44834228 | 44848063 | - | mRNA | protein_coding |
| -114403 | enst00000521529 | sg00000105968 | h2az2-208 | 7 | 44834310 | 44848040 | - | mRNA | protein_coding |
| -114422 | enst00000349299 | sg00000105968 | h2az2-203 | 7 | 44834228 | 44848021 | - | mRNA | protein_coding |
| 118050 | enst00000460409 | sg00000136274 | nacad-201 | 7 | 45080979 | 45081400 | - | lnc_RNA | retained_intron |
| 125619 | enst00000490531 | sg00000136274 | nacad-202 | 7 | 45080437 | 45088969 | - | mRNA | protein_coding |
| 139221 | enst00000482482 | sg00000136270 | tbrg4-211 | 7 | 45101600 | 45102571 | - | lnc_RNA | retained_intron |
| 139340 | enst00000478116 | sg00000136270 | tbrg4-208 | 7 | 45101774 | 45102690 | - | lnc_RNA | retained_intron |
| 140890 | enst00000483615 | sg00000136270 | tbrg4-212 | 7 | 45101503 | 45104240 | - | mRNA | protein_coding |
| 141132 | enst00000384111 | sg00000206838 | snora5a-201 | 7 | 45104349 | 45104482 | - | snoRNA | snorna |
| 141692 | enst00000364902 | sg00000201772 | snora5c-201 | 7 | 45104906 | 45105042 | - | snoRNA | snorna |
| 142128 | enst00000484326 | sg00000136270 | tbrg4-213 | 7 | 45103632 | 45105478 | - | lnc_RNA | retained_intron |
| 142319 | enst00000488222 | sg00000136270 | tbrg4-214 | 7 | 45103031 | 45105669 | - | lnc_RNA | retained_intron |
| 142749 | enst00000363786 | sg00000200656 | snora5b-201 | 7 | 45105968 | 45106099 | - | snoRNA | snorna |
| 144114 | enst00000495973 | sg00000136270 | tbrg4-217 | 7 | 45100101 | 45107464 | - | lnc_RNA | retained_intron |
| 145593 | enst00000477328 | sg00000136270 | tbrg4-207 | 7 | 45105286 | 45108943 | - | lnc_RNA | retained_intron |
| 148151 | enst00000482285 | sg00000136270 | tbrg4-210 | 7 | 45108884 | 45111501 | - | mRNA | protein_coding |
| 148330 | enst00000461363 | sg00000136270 | tbrg4-204 | 7 | 45104538 | 45111680 | - | mRNA | protein_coding |
| 148347 | enst00000495078 | sg00000136270 | tbrg4-216 | 7 | 45108928 | 45111697 | - | mRNA | protein_coding |
| 148347 | enst00000258770 | sg00000136270 | tbrg4-201 | 7 | 45100100 | 45111697 | - | mRNA | protein_coding |
| 148347 | enst00000471142 | sg00000136270 | tbrg4-205 | 7 | 45107751 | 45111697 | - | lnc_RNA | processed_transcript |
| 148356 | enst00000494076 | sg00000136270 | tbrg4-215 | 7 | 45100101 | 45111706 | - | mRNA | protein_coding |
| 148358 | enst00000478532 | sg00000136270 | tbrg4-209 | 7 | 45104209 | 45111708 | - | mRNA | protein_coding |
| 148368 | enst00000361278 | sg00000136270 | tbrg4-202 | 7 | 45100100 | 45111718 | - | mRNA | protein_coding |
| 148671 | enst00000475893 | sg00000136270 | tbrg4-206 | 7 | 45108854 | 45112021 | - | mRNA | protein_coding |
| 148697 | enst00000395655 | sg00000136270 | tbrg4-203 | 7 | 45100100 | 45112047 | - | mRNA | protein_coding |
| -163629 | enst00000480603 | sg00000196262 | ppia-206 | 7 | 44798814 | 44801624 | + | lnc_RNA | processed_transcript |
| -164470 | enst00000494484 | sg00000196262 | ppia-209 | 7 | 44797973 | 44801647 | + | lnc_RNA | retained_intron |
| -165761 | enst00000415933 | sg00000196262 | ppia-202 | 7 | 44796682 | 44801624 | + | mRNA | nonsense_mediated_decay |
| -165762 | enst00000355968 | sg00000196262 | ppia-201 | 7 | 44796681 | 44801631 | + | mRNA | protein_coding |
| -165762 | enst00000489459 | sg00000196262 | ppia-208 | 7 | 44796681 | 44801630 | + | mRNA | protein_coding |
| -165762 | enst00000468812 | sg00000196262 | ppia-204 | 7 | 44796681 | 44803117 | + | mRNA | protein_coding |
| -165762 | enst00000479021 | sg00000196262 | ppia-205 | 7 | 44796681 | 44824564 | + | mRNA | nonsense_mediated_decay |
| -165762 | enst00000620047 | sg00000196262 | ppia-210 | 7 | 44796681 | 44801631 | + | mRNA | protein_coding |
| -165763 | enst00000481437 | sg00000196262 | ppia-207 | 7 | 44796680 | 44799816 | + | lnc_RNA | retained_intron |
| -165763 | enst00000451562 | sg00000196262 | ppia-203 | 7 | 44796680 | 44800011 | + | mRNA | protein_coding |
| -175103 | enst00000425077 | sg00000228596 | ac013436.1-201 | 7 | 44785050 | 44787340 | - | lnc_RNA | lncrna |
| 194441 | enst00000242249 | sg00000122679 | ramp3-201 | 7 | 45157791 | 45184250 | + | mRNA | protein_coding |
| 194479 | enst00000481345 | sg00000122679 | ramp3-202 | 7 | 45157829 | 45186302 | + | mRNA | protein_coding |
| 194479 | enst00000496212 | sg00000122679 | ramp3-203 | 7 | 45157829 | 45186298 | + | mRNA | protein_coding |
| -196699 | enst00000482322 | sg00000122515 | zmiz2-212 | 7 | 44765744 | 44766554 | + | lnc_RNA | retained_intron |
| -196732 | enst00000463931 | sg00000122515 | zmiz2-209 | 7 | 44765711 | 44767617 | + | lnc_RNA | processed_transcript |
| -198754 | enst00000492558 | sg00000122515 | zmiz2-214 | 7 | 44763689 | 44765517 | + | lnc_RNA | processed_transcript |
| -200635 | enst00000480964 | sg00000122515 | zmiz2-211 | 7 | 44761808 | 44765725 | + | lnc_RNA | retained_intron |
| -202492 | enst00000463056 | sg00000122515 | zmiz2-208 | 7 | 44759951 | 44768697 | + | lnc_RNA | retained_intron |
| -202709 | enst00000478045 | sg00000122515 | zmiz2-210 | 7 | 44759734 | 44768688 | + | lnc_RNA | retained_intron |
| -206193 | enst00000615423 | sg00000122515 | zmiz2-215 | 7 | 44756250 | 44767623 | + | mRNA | protein_coding |
| -206238 | enst00000265346 | sg00000122515 | zmiz2-201 | 7 | 44756205 | 44768536 | + | mRNA | protein_coding |
| -206255 | enst00000433667 | sg00000122515 | zmiz2-205 | 7 | 44756188 | 44768694 | + | mRNA | protein_coding |
| -206255 | enst00000492001 | sg00000122515 | zmiz2-213 | 7 | 44756188 | 44756992 | + | lnc_RNA | retained_intron |
| -206264 | enst00000441627 | sg00000122515 | zmiz2-206 | 7 | 44756179 | 44769878 | + | mRNA | protein_coding |
| -213481 | enst00000416856 | sg00000122515 | zmiz2-204 | 7 | 44748962 | 44757561 | + | mRNA | nonsense_mediated_decay |
| -213581 | enst00000457123 | sg00000122515 | zmiz2-207 | 7 | 44748862 | 44757050 | + | mRNA | protein_coding |
| -213596 | enst00000309315 | sg00000122515 | zmiz2-202 | 7 | 44748847 | 44769881 | + | mRNA | protein_coding |
| -213862 | enst00000413916 | sg00000122515 | zmiz2-203 | 7 | 44748581 | 44768694 | + | mRNA | protein_coding |
| -295648 | enst00000497326 | sg00000105953 | ogdh-209 | 7 | 44666795 | 44674752 | + | lnc_RNA | retained_intron |
| -295822 | enst00000459672 | sg00000105953 | ogdh-208 | 7 | 44666621 | 44675245 | + | lnc_RNA | processed_transcript |
| 305331 | enst00000666999 | sg00000286738 | ac073968.2-201 | 7 | 45268681 | 45384802 | + | lnc_RNA | lncrna |
| 340270 | enst00000618594 | sg00000275295 | ac073968.1-201 | 7 | 45303620 | 45304362 | + | pseudogenic_transcript | processed_pseudogene |
| -355815 | enst00000631326 | sg00000105953 | ogdh-210 | 7 | 44606628 | 44708994 | + | mRNA | protein_coding |
| -355815 | enst00000444676 | sg00000105953 | ogdh-205 | 7 | 44606628 | 44708138 | + | mRNA | protein_coding |
| -355816 | enst00000222673 | sg00000105953 | ogdh-201 | 7 | 44606627 | 44709066 | + | mRNA | protein_coding |
| -355848 | enst00000419661 | sg00000105953 | ogdh-202 | 7 | 44606595 | 44666851 | + | mRNA | protein_coding |
| -355852 | enst00000449767 | sg00000105953 | ogdh-207 | 7 | 44606591 | 44708328 | + | mRNA | protein_coding |
| -355852 | enst00000447398 | sg00000105953 | ogdh-206 | 7 | 44606591 | 44708278 | + | mRNA | protein_coding |
| -355855 | enst00000443864 | sg00000105953 | ogdh-204 | 7 | 44606588 | 44676594 | + | mRNA | protein_coding |
| -355871 | enst00000439616 | sg00000105953 | ogdh-203 | 7 | 44606572 | 44708230 | + | mRNA | protein_coding |
| -361411 | enst00000603255 | sg00000271586 | ac011894.1-201 | 7 | 44601032 | 44601487 | + | pseudogenic_transcript | processed_pseudogene |
| -379924 | enst00000658337 | sg00000287574 | ac004938.2-201 | 7 | 44582519 | 44583676 | + | lnc_RNA | lncrna |
| -380156 | enst00000289577 | sg00000158604 | tmed4-201 | 7 | 44577894 | 44582287 | - | mRNA | protein_coding |
| -380202 | enst00000444131 | sg00000158604 | tmed4-202 | 7 | 44581093 | 44582241 | - | lnc_RNA | processed_transcript |
| -380212 | enst00000481238 | sg00000158604 | tmed4-205 | 7 | 44579897 | 44582231 | - | mRNA | protein_coding |
| -380212 | enst00000457408 | sg00000158604 | tmed4-203 | 7 | 44577894 | 44582231 | - | mRNA | protein_coding |
| -380233 | enst00000477639 | sg00000158604 | tmed4-204 | 7 | 44579904 | 44582210 | - | lnc_RNA | retained_intron |
| -387392 | enst00000421223 | sg00000136271 | ddx56-203 | 7 | 44565805 | 44575051 | - | mRNA | nonsense_mediated_decay |
| -388441 | enst00000258772 | sg00000136271 | ddx56-201 | 7 | 44565417 | 44574002 | - | mRNA | protein_coding |
| -388518 | enst00000479440 | sg00000136271 | ddx56-210 | 7 | 44572650 | 44573925 | - | lnc_RNA | retained_intron |
| -388518 | enst00000431640 | sg00000136271 | ddx56-204 | 7 | 44566002 | 44573925 | - | mRNA | protein_coding |
| -388535 | enst00000415758 | sg00000136271 | ddx56-202 | 7 | 44568216 | 44573908 | - | mRNA | nonsense_mediated_decay |
| -388548 | enst00000446987 | sg00000136271 | ddx56-206 | 7 | 44565804 | 44573895 | - | mRNA | nonsense_mediated_decay |
| -388685 | enst00000485367 | sg00000136271 | ddx56-212 | 7 | 44565819 | 44573758 | - | lnc_RNA | processed_transcript |
| -388779 | enst00000467318 | sg00000136271 | ddx56-208 | 7 | 44565837 | 44573664 | - | lnc_RNA | processed_transcript |
| -388779 | enst00000433257 | sg00000136271 | ddx56-205 | 7 | 44565837 | 44573664 | - | mRNA | nonsense_mediated_decay |
| -391678 | enst00000473924 | sg00000136271 | ddx56-209 | 7 | 44569752 | 44570765 | - | lnc_RNA | retained_intron |
| -392601 | enst00000448192 | sg00000136271 | ddx56-207 | 7 | 44566138 | 44569842 | - | mRNA | protein_coding |
| -394661 | enst00000479602 | sg00000136271 | ddx56-211 | 7 | 44565807 | 44567782 | - | lnc_RNA | processed_transcript |
| -421128 | enst00000423141 | sg00000015520 | npc1l1-203 | 7 | 44533227 | 44541315 | - | mRNA | protein_coding |
| -421128 | enst00000381160 | sg00000015520 | npc1l1-202 | 7 | 44513361 | 44541315 | - | mRNA | protein_coding |
| -421128 | enst00000546276 | sg00000015520 | npc1l1-204 | 7 | 44512538 | 44541315 | - | mRNA | protein_coding |
| -421128 | enst00000289547 | sg00000015520 | npc1l1-201 | 7 | 44512535 | 44541315 | - | mRNA | protein_coding |
| 428855 | enst00000485699 | sg00000234359 | elk1p1-201 | 7 | 45391626 | 45392205 | - | pseudogenic_transcript | processed_pseudogene |
| -451111 | enst00000438468 | sg00000225443 | ac004938.1-201 | 7 | 44511025 | 44511332 | - | pseudogenic_transcript | processed_pseudogene |
| -458564 | enst00000363586 | sg00000200456 | rnu6-1097p-201 | 7 | 44503773 | 44503879 | - | snRNA | snrna |
| -471785 | enst00000355451 | sg00000015676 | nudcd3-202 | 7 | 44379119 | 44490658 | - | mRNA | protein_coding |
| -471837 | enst00000464812 | sg00000015676 | nudcd3-204 | 7 | 44404513 | 44490606 | - | lnc_RNA | retained_intron |
| -472178 | enst00000497978 | sg00000015676 | nudcd3-211 | 7 | 44485069 | 44490265 | - | lnc_RNA | processed_transcript |
| -477169 | enst00000480209 | sg00000015676 | nudcd3-208 | 7 | 44484444 | 44485274 | - | lnc_RNA | processed_transcript |
| -480981 | enst00000460110 | sg00000015676 | nudcd3-203 | 7 | 44383591 | 44481462 | - | lnc_RNA | processed_transcript |
| -490483 | enst00000472246 | sg00000015676 | nudcd3-205 | 7 | 44392385 | 44471960 | - | lnc_RNA | processed_transcript |
| -494546 | enst00000487895 | sg00000146677 | ac004453.1-201 | 7 | 44467897 | 44468304 | + | pseudogenic_transcript | processed_pseudogene |
| 497362 | enst00000443714 | sg00000225537 | ac073325.1-201 | 7 | 45460712 | 45542182 | + | lnc_RNA | lncrna |
Source file: /hps/research1/birney/users/adrien/analyses/cancer_DNA_promethion/run_1_2_3_4/DNA_pipeline_2/results/methylation/pycometh_meth_comp_CGI_3/out.tsv.gz
MD5 hash: 9aa0e3f69cb4e12345c3758eb68a5efc