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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 |
|---|---|---|---|---|---|---|---|---|
| #98 | 19 | 5058595 | 5059854 | 1259 | 3 | 39 | 1.21616e-17 | 1.23415e-15 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| 10764 | enst00000589104 | sg00000127663 | kdm4b-208 | 19 | 5070618 | 5151924 | + | lnc_RNA | retained_intron |
| -11597 | enst00000592175 | sg00000127663 | kdm4b-210 | 19 | 5046998 | 5082437 | + | lnc_RNA | processed_transcript |
| 14237 | enst00000624683 | sg00000127663 | kdm4b-212 | 19 | 5074091 | 5079166 | + | unconfirmed_transcript | tec |
| 20834 | enst00000588961 | sg00000127663 | kdm4b-207 | 19 | 5080688 | 5110734 | + | lnc_RNA | processed_transcript |
| 22598 | enst00000588361 | sg00000127663 | kdm4b-206 | 19 | 5082452 | 5141503 | + | mRNA | protein_coding |
| -42270 | enst00000536461 | sg00000127663 | kdm4b-203 | 19 | 5016325 | 5153105 | + | mRNA | protein_coding |
| 52504 | enst00000592159 | sg00000127663 | kdm4b-209 | 19 | 5112358 | 5119682 | + | lnc_RNA | processed_transcript |
| 75682 | enst00000588166 | sg00000127663 | kdm4b-204 | 19 | 5135536 | 5138470 | + | lnc_RNA | processed_transcript |
| -89463 | enst00000381759 | sg00000127663 | kdm4b-202 | 19 | 4969132 | 5113340 | + | mRNA | protein_coding |
| -89481 | enst00000588337 | sg00000127663 | kdm4b-205 | 19 | 4969114 | 5041181 | + | mRNA | protein_coding |
| -89482 | enst00000159111 | sg00000127663 | kdm4b-201 | 19 | 4969113 | 5153598 | + | mRNA | protein_coding |
| -89482 | enst00000611640 | sg00000127663 | kdm4b-211 | 19 | 4969113 | 5153595 | + | mRNA | protein_coding |
| 118265 | enst00000592429 | sg00000267550 | ac022517.1-201 | 19 | 5178119 | 5178464 | + | lnc_RNA | lncrna |
| -125908 | enst00000584057 | sg00000263409 | mir4747-201 | 19 | 4932687 | 4932740 | + | miRNA | mirna |
| -148220 | enst00000616255 | sg00000276043 | uhrf1-204 | 19 | 4910375 | 4960952 | + | mRNA | protein_coding |
| -148228 | enst00000622802 | sg00000276043 | uhrf1-206 | 19 | 4910367 | 4961132 | + | mRNA | protein_coding |
| -148449 | enst00000615884 | sg00000276043 | uhrf1-203 | 19 | 4910146 | 4960961 | + | mRNA | protein_coding |
| -149094 | enst00000650932 | sg00000276043 | uhrf1-208 | 19 | 4909501 | 4962154 | + | mRNA | protein_coding |
| -149097 | enst00000624301 | sg00000276043 | uhrf1-207 | 19 | 4909498 | 4962151 | + | mRNA | protein_coding |
| -149097 | enst00000613817 | sg00000276043 | uhrf1-202 | 19 | 4909498 | 4961171 | + | mRNA | protein_coding |
| -149165 | enst00000620565 | sg00000276043 | uhrf1-205 | 19 | 4909430 | 4962150 | + | mRNA | protein_coding |
| -155515 | enst00000612630 | sg00000276043 | uhrf1-201 | 19 | 4903080 | 4962154 | + | mRNA | protein_coding |
| -155699 | enst00000650722 | sg00000205784 | arrdc5-202 | 19 | 4890437 | 4902896 | - | mRNA | protein_coding |
| -155728 | enst00000381781 | sg00000205784 | arrdc5-201 | 19 | 4890437 | 4902867 | - | mRNA | protein_coding |
| 160162 | enst00000589851 | sg00000105426 | ptprs-207 | 19 | 5215367 | 5220016 | - | lnc_RNA | retained_intron |
| -190901 | enst00000585479 | sg00000105355 | plin3-202 | 19 | 4839062 | 4867694 | - | mRNA | protein_coding |
| -190928 | enst00000221957 | sg00000105355 | plin3-201 | 19 | 4838341 | 4867667 | - | mRNA | protein_coding |
| -190932 | enst00000589494 | sg00000105355 | plin3-206 | 19 | 4852208 | 4867663 | - | mRNA | protein_coding |
| -190942 | enst00000592528 | sg00000105355 | plin3-207 | 19 | 4838369 | 4867653 | - | mRNA | protein_coding |
| -190958 | enst00000589034 | sg00000105355 | plin3-204 | 19 | 4852039 | 4867637 | - | mRNA | protein_coding |
| -191483 | enst00000587462 | sg00000105355 | plin3-203 | 19 | 4859984 | 4867112 | - | mRNA | protein_coding |
| -198959 | enst00000589163 | sg00000105355 | plin3-205 | 19 | 4838371 | 4859636 | - | mRNA | protein_coding |
| 217880 | enst00000486380 | sg00000239524 | rpl32p34-201 | 19 | 5277734 | 5278133 | + | pseudogenic_transcript | processed_pseudogene |
| -220263 | enst00000591657 | sg00000267484 | ac027319.1-201 | 19 | 4838332 | 4838907 | + | lnc_RNA | lncrna |
| 226286 | enst00000353284 | sg00000105426 | ptprs-202 | 19 | 5206774 | 5286140 | - | mRNA | protein_coding |
| 226309 | enst00000262963 | sg00000105426 | ptprs-201 | 19 | 5206537 | 5286163 | - | mRNA | protein_coding |
| 226309 | enst00000588012 | sg00000105426 | ptprs-205 | 19 | 5206537 | 5286163 | - | mRNA | protein_coding |
| 226309 | enst00000592099 | sg00000105426 | ptprs-210 | 19 | 5206537 | 5286163 | - | mRNA | protein_coding |
| 226386 | enst00000587303 | sg00000105426 | ptprs-204 | 19 | 5206368 | 5286240 | - | mRNA | protein_coding |
| 226534 | enst00000590509 | sg00000105426 | ptprs-208 | 19 | 5273061 | 5286388 | - | mRNA | protein_coding |
| -226891 | enst00000248244 | sg00000127666 | ticam1-201 | 19 | 4815932 | 4831704 | - | mRNA | protein_coding |
| 232933 | enst00000586065 | sg00000105426 | ptprs-203 | 19 | 5274199 | 5292787 | - | mRNA | protein_coding |
| 233398 | enst00000591760 | sg00000105426 | ptprs-209 | 19 | 5273549 | 5293252 | - | mRNA | protein_coding |
| 234393 | enst00000619774 | sg00000274447 | ac005790.1-201 | 19 | 5294247 | 5294696 | + | lnc_RNA | lncrna |
| -240625 | enst00000621756 | sg00000127666 | ticam1-202 | 19 | 4816235 | 4817970 | - | mRNA | protein_coding |
| -263036 | enst00000596170 | sg00000269604 | ac005523.2-202 | 19 | 4794982 | 4795559 | - | lnc_RNA | lncrna |
| -263040 | enst00000601192 | sg00000269604 | ac005523.2-201 | 19 | 4791745 | 4795555 | - | lnc_RNA | lncrna |
| -266861 | enst00000269856 | sg00000141965 | fem1a-201 | 19 | 4791734 | 4801273 | + | mRNA | protein_coding |
| -267388 | enst00000598782 | sg00000268536 | ac005523.1-201 | 19 | 4785120 | 4791207 | - | lnc_RNA | lncrna |
| 280949 | enst00000588552 | sg00000105426 | ptprs-206 | 19 | 5158495 | 5340803 | - | lnc_RNA | processed_transcript |
| -287925 | enst00000384898 | sg00000207630 | mir7-3-201 | 19 | 4770670 | 4770779 | + | miRNA | mirna |
| -288446 | enst00000588923 | sg00000176840 | mir7-3hg-205 | 19 | 4770149 | 4772537 | + | lnc_RNA | lncrna |
| -288522 | enst00000662608 | sg00000176840 | mir7-3hg-230 | 19 | 4770073 | 4772468 | + | lnc_RNA | lncrna |
| -289314 | enst00000588758 | sg00000176840 | mir7-3hg-204 | 19 | 4769281 | 4772517 | + | lnc_RNA | lncrna |
| -289428 | enst00000589639 | sg00000176840 | mir7-3hg-207 | 19 | 4769167 | 4772414 | + | lnc_RNA | lncrna |
| -289454 | enst00000592709 | sg00000176840 | mir7-3hg-210 | 19 | 4769141 | 4772517 | + | lnc_RNA | lncrna |
| -289460 | enst00000670131 | sg00000176840 | mir7-3hg-248 | 19 | 4769135 | 4772537 | + | lnc_RNA | lncrna |
| -289460 | enst00000669408 | sg00000176840 | mir7-3hg-245 | 19 | 4769135 | 4772537 | + | lnc_RNA | lncrna |
| -289462 | enst00000669700 | sg00000176840 | mir7-3hg-246 | 19 | 4769133 | 4785077 | + | lnc_RNA | lncrna |
| -289462 | enst00000653316 | sg00000176840 | mir7-3hg-212 | 19 | 4769133 | 4781238 | + | lnc_RNA | lncrna |
| -289462 | enst00000660889 | sg00000176840 | mir7-3hg-227 | 19 | 4769133 | 4772557 | + | lnc_RNA | lncrna |
| -289462 | enst00000667215 | sg00000176840 | mir7-3hg-240 | 19 | 4769133 | 4772556 | + | lnc_RNA | lncrna |
| -289462 | enst00000660172 | sg00000176840 | mir7-3hg-226 | 19 | 4769133 | 4772556 | + | lnc_RNA | lncrna |
| -289462 | enst00000657100 | sg00000176840 | mir7-3hg-222 | 19 | 4769133 | 4772555 | + | lnc_RNA | lncrna |
| -289462 | enst00000317292 | sg00000176840 | mir7-3hg-201 | 19 | 4769133 | 4772555 | + | lnc_RNA | lncrna |
| -289462 | enst00000653355 | sg00000176840 | mir7-3hg-213 | 19 | 4769133 | 4772553 | + | lnc_RNA | lncrna |
| -289462 | enst00000670508 | sg00000176840 | mir7-3hg-249 | 19 | 4769133 | 4772537 | + | lnc_RNA | lncrna |
| -289462 | enst00000655494 | sg00000176840 | mir7-3hg-219 | 19 | 4769133 | 4772560 | + | lnc_RNA | lncrna |
| -289462 | enst00000669248 | sg00000176840 | mir7-3hg-244 | 19 | 4769133 | 4772537 | + | lnc_RNA | lncrna |
| -289462 | enst00000667223 | sg00000176840 | mir7-3hg-241 | 19 | 4769133 | 4772537 | + | lnc_RNA | lncrna |
| -289462 | enst00000667444 | sg00000176840 | mir7-3hg-242 | 19 | 4769133 | 4772537 | + | lnc_RNA | lncrna |
| -289462 | enst00000656089 | sg00000176840 | mir7-3hg-220 | 19 | 4769133 | 4771541 | + | lnc_RNA | lncrna |
| -289462 | enst00000592663 | sg00000176840 | mir7-3hg-209 | 19 | 4769133 | 4772516 | + | lnc_RNA | lncrna |
| -289462 | enst00000658545 | sg00000176840 | mir7-3hg-224 | 19 | 4769133 | 4772517 | + | lnc_RNA | lncrna |
| -289462 | enst00000669889 | sg00000176840 | mir7-3hg-247 | 19 | 4769133 | 4772517 | + | lnc_RNA | lncrna |
| -289462 | enst00000657474 | sg00000176840 | mir7-3hg-223 | 19 | 4769133 | 4772536 | + | lnc_RNA | lncrna |
| -289462 | enst00000586721 | sg00000176840 | mir7-3hg-202 | 19 | 4769133 | 4772537 | + | lnc_RNA | lncrna |
| -289462 | enst00000588711 | sg00000176840 | mir7-3hg-203 | 19 | 4769133 | 4772537 | + | lnc_RNA | lncrna |
| -289462 | enst00000589368 | sg00000176840 | mir7-3hg-206 | 19 | 4769133 | 4772537 | + | lnc_RNA | lncrna |
| -289462 | enst00000591008 | sg00000176840 | mir7-3hg-208 | 19 | 4769133 | 4772537 | + | lnc_RNA | lncrna |
| -289462 | enst00000653012 | sg00000176840 | mir7-3hg-211 | 19 | 4769133 | 4772537 | + | lnc_RNA | lncrna |
| -289462 | enst00000666837 | sg00000176840 | mir7-3hg-238 | 19 | 4769133 | 4772537 | + | lnc_RNA | lncrna |
| -289462 | enst00000654084 | sg00000176840 | mir7-3hg-215 | 19 | 4769133 | 4772537 | + | lnc_RNA | lncrna |
| -289462 | enst00000655375 | sg00000176840 | mir7-3hg-218 | 19 | 4769133 | 4772537 | + | lnc_RNA | lncrna |
| -289462 | enst00000656469 | sg00000176840 | mir7-3hg-221 | 19 | 4769133 | 4772537 | + | lnc_RNA | lncrna |
| -289462 | enst00000660973 | sg00000176840 | mir7-3hg-228 | 19 | 4769133 | 4772537 | + | lnc_RNA | lncrna |
| -289462 | enst00000661584 | sg00000176840 | mir7-3hg-229 | 19 | 4769133 | 4772537 | + | lnc_RNA | lncrna |
| -289462 | enst00000663010 | sg00000176840 | mir7-3hg-232 | 19 | 4769133 | 4772537 | + | lnc_RNA | lncrna |
| -289462 | enst00000663804 | sg00000176840 | mir7-3hg-234 | 19 | 4769133 | 4772537 | + | lnc_RNA | lncrna |
| -289462 | enst00000664951 | sg00000176840 | mir7-3hg-235 | 19 | 4769133 | 4772537 | + | lnc_RNA | lncrna |
| -289462 | enst00000665092 | sg00000176840 | mir7-3hg-236 | 19 | 4769133 | 4772537 | + | lnc_RNA | lncrna |
| -289462 | enst00000666056 | sg00000176840 | mir7-3hg-237 | 19 | 4769133 | 4772537 | + | lnc_RNA | lncrna |
| -289462 | enst00000653646 | sg00000176840 | mir7-3hg-214 | 19 | 4769133 | 4772537 | + | lnc_RNA | lncrna |
| -289462 | enst00000666978 | sg00000176840 | mir7-3hg-239 | 19 | 4769133 | 4772537 | + | lnc_RNA | lncrna |
| -289463 | enst00000654534 | sg00000176840 | mir7-3hg-216 | 19 | 4769132 | 4781240 | + | lnc_RNA | lncrna |
| -289463 | enst00000668602 | sg00000176840 | mir7-3hg-243 | 19 | 4769132 | 4772556 | + | lnc_RNA | lncrna |
| -289463 | enst00000662725 | sg00000176840 | mir7-3hg-231 | 19 | 4769132 | 4772537 | + | lnc_RNA | lncrna |
| -289499 | enst00000663176 | sg00000176840 | mir7-3hg-233 | 19 | 4769096 | 4781240 | + | lnc_RNA | lncrna |
| -289516 | enst00000655163 | sg00000176840 | mir7-3hg-217 | 19 | 4769079 | 4772555 | + | lnc_RNA | lncrna |
| -289564 | enst00000658818 | sg00000176840 | mir7-3hg-225 | 19 | 4769031 | 4772537 | + | lnc_RNA | lncrna |
| -333922 | enst00000598041 | sg00000142002 | dpp9-212 | 19 | 4714106 | 4724673 | - | mRNA | protein_coding |
| -334732 | enst00000262960 | sg00000142002 | dpp9-201 | 19 | 4675226 | 4723863 | - | mRNA | protein_coding |
| -334753 | enst00000597726 | sg00000142002 | dpp9-209 | 19 | 4702684 | 4723842 | - | mRNA | protein_coding |
| -334753 | enst00000601130 | sg00000142002 | dpp9-221 | 19 | 4714161 | 4723842 | - | mRNA | protein_coding |
| -334760 | enst00000602161 | sg00000142002 | dpp9-225 | 19 | 4705915 | 4723835 | - | mRNA | protein_coding |
| -334765 | enst00000595940 | sg00000142002 | dpp9-205 | 19 | 4714187 | 4723830 | - | lnc_RNA | processed_transcript |
| -334775 | enst00000600556 | sg00000142002 | dpp9-219 | 19 | 4705899 | 4723820 | - | mRNA | nonsense_mediated_decay |
| -334782 | enst00000601764 | sg00000142002 | dpp9-224 | 19 | 4694318 | 4723813 | - | lnc_RNA | retained_intron |
| -334789 | enst00000598800 | sg00000142002 | dpp9-214 | 19 | 4676564 | 4723806 | - | mRNA | protein_coding |
| -334798 | enst00000597024 | sg00000142002 | dpp9-206 | 19 | 4719618 | 4723797 | - | lnc_RNA | processed_transcript |
| -334813 | enst00000600497 | sg00000142002 | dpp9-218 | 19 | 4715890 | 4723782 | - | lnc_RNA | processed_transcript |
| -334845 | enst00000597849 | sg00000142002 | dpp9-210 | 19 | 4694317 | 4723750 | - | mRNA | protein_coding |
| -335823 | enst00000600621 | sg00000142002 | dpp9-220 | 19 | 4705863 | 4722772 | - | mRNA | protein_coding |
| -335864 | enst00000598360 | sg00000142002 | dpp9-213 | 19 | 4705926 | 4722731 | - | mRNA | protein_coding |
| -340707 | enst00000599248 | sg00000142002 | dpp9-216 | 19 | 4714204 | 4717888 | - | mRNA | protein_coding |
| -342468 | enst00000593973 | sg00000142002 | dpp9-202 | 19 | 4714246 | 4716127 | - | mRNA | protein_coding |
| -344289 | enst00000594671 | sg00000142002 | dpp9-203 | 19 | 4675224 | 4714306 | - | mRNA | protein_coding |
| -344375 | enst00000597145 | sg00000142002 | dpp9-207 | 19 | 4675764 | 4714220 | - | lnc_RNA | retained_intron |
| -354444 | enst00000599163 | sg00000142002 | dpp9-215 | 19 | 4690878 | 4704151 | - | mRNA | nonsense_mediated_decay |
| -363501 | enst00000599998 | sg00000142002 | dpp9-217 | 19 | 4689656 | 4695094 | - | lnc_RNA | retained_intron |
| -363860 | enst00000597253 | sg00000142002 | dpp9-208 | 19 | 4688292 | 4694735 | - | lnc_RNA | retained_intron |
| -366574 | enst00000655857 | sg00000287884 | ac005594.1-201 | 19 | 4692021 | 4694340 | + | lnc_RNA | lncrna |
| -367689 | enst00000595327 | sg00000142002 | dpp9-204 | 19 | 4685628 | 4690906 | - | mRNA | protein_coding |
| -369792 | enst00000601720 | sg00000142002 | dpp9-223 | 19 | 4676464 | 4688803 | - | mRNA | protein_coding |
| -372848 | enst00000597900 | sg00000142002 | dpp9-211 | 19 | 4679837 | 4685747 | - | mRNA | nonsense_mediated_decay |
| -372912 | enst00000646573 | sg00000142002 | dpp9-226 | 19 | 4679835 | 4685683 | - | mRNA | nonsense_mediated_decay |
| -373785 | enst00000601173 | sg00000142002 | dpp9-222 | 19 | 4682944 | 4684810 | - | lnc_RNA | processed_transcript |
| -379313 | enst00000381796 | sg00000205790 | dpp9-as1-201 | 19 | 4679282 | 4685948 | + | lnc_RNA | lncrna |
| -388233 | enst00000599630 | sg00000074842 | mydgf-203 | 19 | 4659688 | 4670362 | - | mRNA | protein_coding |
| -388253 | enst00000262947 | sg00000074842 | mydgf-201 | 19 | 4657545 | 4670342 | - | mRNA | protein_coding |
| -389899 | enst00000596031 | sg00000074842 | mydgf-202 | 19 | 4660580 | 4668696 | - | lnc_RNA | retained_intron |
| -393689 | enst00000599761 | sg00000074842 | mydgf-204 | 19 | 4641374 | 4664906 | - | mRNA | protein_coding |
| 395563 | enst00000222033 | sg00000105428 | znrf4-201 | 19 | 5455417 | 5456856 | + | mRNA | protein_coding |
| -403071 | enst00000598070 | sg00000268565 | ac005339.1-201 | 19 | 4654964 | 4655524 | - | lnc_RNA | lncrna |
| -418578 | enst00000536716 | sg00000185361 | tnfaip8l1-202 | 19 | 4640017 | 4655568 | + | mRNA | protein_coding |
| -419058 | enst00000598107 | sg00000185361 | tnfaip8l1-203 | 19 | 4639537 | 4642482 | + | lnc_RNA | processed_transcript |
| -419079 | enst00000327473 | sg00000185361 | tnfaip8l1-201 | 19 | 4639516 | 4655568 | + | mRNA | protein_coding |
| -437401 | enst00000592027 | sg00000267408 | ac011498.5-201 | 19 | 4621194 | 4622307 | + | pseudogenic_transcript | unprocessed_pseudogene |
| -498911 | enst00000586582 | sg00000167680 | sema6b-201 | 19 | 4542593 | 4559684 | - | mRNA | protein_coding |
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