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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 |
|---|---|---|---|---|---|---|---|---|
| #170 | 17 | 31008224 | 31009540 | 1316 | 3 | 37 | 9.26473e-15 | 5.41987e-13 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| 0 | enst00000579692 | sg00000266865 | ac138207.8-201 | 17 | 31008497 | 31022341 | + | lnc_RNA | processed_transcript |
| 0 | enst00000585289 | sg00000264148 | ac138207.3-201 | 17 | 31008154 | 31008319 | - | pseudogenic_transcript | processed_pseudogene |
| 0 | enst00000580190 | sg00000266865 | ac138207.8-202 | 17 | 31008605 | 31045549 | + | lnc_RNA | processed_transcript |
| 0 | enst00000582483 | sg00000266865 | ac138207.8-203 | 17 | 31008674 | 31029471 | + | lnc_RNA | processed_transcript |
| 0 | enst00000579588 | sg00000266865 | ac138207.8-204 | 17 | 31008754 | 31031946 | + | pseudogenic_transcript | transcribed_unprocessed_pseudogene |
| 14801 | enst00000578883 | sg00000266865 | ac138207.8-205 | 17 | 31024341 | 31034162 | + | lnc_RNA | processed_transcript |
| -20147 | enst00000434242 | sg00000181481 | rnf135-203 | 17 | 30988077 | 30997528 | + | mRNA | protein_coding |
| -27974 | enst00000584499 | sg00000266340 | ac138207.7-201 | 17 | 30978610 | 30980250 | - | lnc_RNA | lncrna |
| -32837 | enst00000578053 | sg00000264743 | dprxp4-201 | 17 | 30975387 | 30975954 | + | pseudogenic_transcript | processed_pseudogene |
| 35867 | enst00000580053 | sg00000266865 | ac138207.8-206 | 17 | 31045407 | 31093127 | + | lnc_RNA | processed_transcript |
| -36572 | enst00000580979 | sg00000264456 | ac138207.4-201 | 17 | 30971652 | 30973312 | + | lnc_RNA | lncrna |
| -37083 | enst00000580444 | sg00000181481 | rnf135-206 | 17 | 30971141 | 30997248 | + | mRNA | protein_coding |
| -37164 | enst00000535306 | sg00000181481 | rnf135-205 | 17 | 30971060 | 30999911 | + | mRNA | protein_coding |
| -37185 | enst00000328381 | sg00000181481 | rnf135-202 | 17 | 30971039 | 30999911 | + | mRNA | protein_coding |
| -37201 | enst00000324689 | sg00000181481 | rnf135-201 | 17 | 30971023 | 30999909 | + | mRNA | protein_coding |
| -37240 | enst00000443677 | sg00000181481 | rnf135-204 | 17 | 30970984 | 30999370 | + | mRNA | protein_coding |
| 38180 | enst00000583112 | sg00000265798 | ac138207.6-202 | 17 | 31041088 | 31047720 | - | lnc_RNA | processed_transcript |
| -39439 | enst00000582674 | sg00000286194 | ac138207.9-201 | 17 | 30968785 | 30970307 | + | lnc_RNA | lncrna |
| 41486 | enst00000579164 | sg00000265798 | ac138207.6-201 | 17 | 31038575 | 31051026 | - | pseudogenic_transcript | transcribed_unprocessed_pseudogene |
| -42724 | enst00000579561 | sg00000265743 | ac138207.5-201 | 17 | 30964935 | 30965500 | - | lnc_RNA | lncrna |
| -48660 | enst00000577405 | sg00000266274 | rn7sl138p-201 | 17 | 30959564 | 30959850 | + | ncRNA | misc_rna |
| 49581 | enst00000581652 | sg00000265798 | ac138207.6-203 | 17 | 31041971 | 31059121 | - | lnc_RNA | processed_transcript |
| -51263 | enst00000442757 | sg00000230113 | ac138207.1-201 | 17 | 30956280 | 30956961 | - | lnc_RNA | lncrna |
| -53970 | enst00000470962 | sg00000184060 | adap2-202 | 17 | 30954254 | 30958141 | + | lnc_RNA | retained_intron |
| -53984 | enst00000480980 | sg00000184060 | adap2-203 | 17 | 30954240 | 30956728 | + | lnc_RNA | retained_intron |
| -63182 | enst00000584989 | sg00000184060 | adap2-210 | 17 | 30945042 | 30956362 | + | mRNA | protein_coding |
| -63196 | enst00000584828 | sg00000184060 | adap2-209 | 17 | 30945028 | 30958339 | + | mRNA | protein_coding |
| 84885 | enst00000578268 | sg00000265444 | mir4733-201 | 17 | 31094350 | 31094425 | - | miRNA | mirna |
| 85387 | enst00000487476 | sg00000196712 | nf1-211 | 17 | 31094927 | 31219359 | + | mRNA | protein_coding |
| 85387 | enst00000356175 | sg00000196712 | nf1-201 | 17 | 31094927 | 31377677 | + | mRNA | protein_coding |
| 85437 | enst00000431387 | sg00000196712 | nf1-204 | 17 | 31094977 | 31222764 | + | mRNA | protein_coding |
| 85437 | enst00000358273 | sg00000196712 | nf1-202 | 17 | 31094977 | 31377675 | + | mRNA | protein_coding |
| 85668 | enst00000579081 | sg00000196712 | nf1-219 | 17 | 31095208 | 31374287 | + | mRNA | nonsense_mediated_decay |
| 85910 | enst00000583377 | sg00000264107 | ac138207.2-201 | 17 | 31090787 | 31095450 | - | lnc_RNA | lncrna |
| -86276 | enst00000580526 | sg00000184060 | adap2-205 | 17 | 30921948 | 30949330 | + | mRNA | nonsense_mediated_decay |
| -86279 | enst00000330889 | sg00000184060 | adap2-201 | 17 | 30921945 | 30959322 | + | mRNA | protein_coding |
| -86289 | enst00000581285 | sg00000184060 | adap2-206 | 17 | 30921935 | 30956442 | + | mRNA | protein_coding |
| -86292 | enst00000580525 | sg00000184060 | adap2-204 | 17 | 30921932 | 30958220 | + | mRNA | protein_coding |
| -86307 | enst00000581548 | sg00000184060 | adap2-207 | 17 | 30921917 | 30949338 | + | mRNA | protein_coding |
| -86544 | enst00000585130 | sg00000184060 | adap2-211 | 17 | 30921680 | 30958739 | + | mRNA | nonsense_mediated_decay |
| -101880 | enst00000583688 | sg00000184060 | adap2-208 | 17 | 30906344 | 30921760 | + | lnc_RNA | processed_transcript |
| -101986 | enst00000581216 | sg00000172171 | tefm-205 | 17 | 30898986 | 30906238 | - | mRNA | protein_coding |
| -101989 | enst00000541382 | sg00000172171 | tefm-202 | 17 | 30904039 | 30906235 | - | lnc_RNA | retained_intron |
| -101989 | enst00000580840 | sg00000172171 | tefm-204 | 17 | 30898986 | 30906235 | - | mRNA | protein_coding |
| -101989 | enst00000306049 | sg00000172171 | tefm-201 | 17 | 30898986 | 30906235 | - | mRNA | nonsense_mediated_decay |
| -109109 | enst00000579183 | sg00000172171 | tefm-203 | 17 | 30897336 | 30899115 | - | lnc_RNA | processed_transcript |
| -109114 | enst00000614165 | sg00000275185 | ac130324.3-201 | 17 | 30899110 | 30899651 | + | lnc_RNA | lncrna |
| 118918 | enst00000489712 | sg00000196712 | nf1-213 | 17 | 31128458 | 31169964 | + | lnc_RNA | processed_transcript |
| 123642 | enst00000584382 | sg00000266371 | ac079915.1-201 | 17 | 31133182 | 31138518 | + | lnc_RNA | lncrna |
| -143284 | enst00000584157 | sg00000263531 | ac130324.1-201 | 17 | 30863921 | 30864940 | - | lnc_RNA | lncrna |
| -145196 | enst00000580873 | sg00000265334 | ac130324.2-201 | 17 | 30834325 | 30863028 | - | lnc_RNA | lncrna |
| -146381 | enst00000390888 | sg00000212190 | rnu6-298p-201 | 17 | 30861843 | 30861938 | + | snRNA | snrna |
| 146501 | enst00000495910 | sg00000196712 | nf1-216 | 17 | 31156041 | 31254292 | + | mRNA | nonsense_mediated_decay |
| 149525 | enst00000490416 | sg00000196712 | nf1-214 | 17 | 31159065 | 31183472 | + | mRNA | protein_coding |
| -173015 | enst00000585133 | sg00000176208 | atad5-203 | 17 | 30835209 | 30869852 | + | lnc_RNA | retained_intron |
| -176254 | enst00000578295 | sg00000176208 | atad5-202 | 17 | 30831970 | 30876439 | + | mRNA | non_stop_decay |
| -176258 | enst00000321990 | sg00000176208 | atad5-201 | 17 | 30831966 | 30895869 | + | mRNA | protein_coding |
| -177323 | enst00000490847 | sg00000242439 | ac127024.1-201 | 17 | 30830901 | 30831318 | + | pseudogenic_transcript | processed_pseudogene |
| -183532 | enst00000324238 | sg00000176390 | crlf3-201 | 17 | 30782684 | 30824692 | - | mRNA | protein_coding |
| -183553 | enst00000578692 | sg00000176390 | crlf3-203 | 17 | 30783936 | 30824671 | - | mRNA | nonsense_mediated_decay |
| 190996 | enst00000456735 | sg00000196712 | nf1-205 | 17 | 31200536 | 31374433 | + | mRNA | protein_coding |
| -198238 | enst00000583805 | sg00000176390 | crlf3-205 | 17 | 30803927 | 30809986 | - | lnc_RNA | processed_transcript |
| -204570 | enst00000621598 | sg00000276250 | ac127024.6-201 | 17 | 30803654 | 30804077 | + | lnc_RNA | lncrna |
| -206804 | enst00000577725 | sg00000176390 | crlf3-202 | 17 | 30785107 | 30801420 | - | lnc_RNA | processed_transcript |
| 215543 | enst00000493220 | sg00000196712 | nf1-215 | 17 | 31225083 | 31331904 | + | lnc_RNA | retained_intron |
| -215852 | enst00000580085 | sg00000266490 | ac127024.5-201 | 17 | 30792372 | 30792833 | + | lnc_RNA | lncrna |
| -222231 | enst00000583527 | sg00000176390 | crlf3-204 | 17 | 30772363 | 30785993 | - | mRNA | protein_coding |
| 223490 | enst00000466819 | sg00000196712 | nf1-206 | 17 | 31233030 | 31261794 | + | mRNA | nonsense_mediated_decay |
| 223490 | enst00000479614 | sg00000196712 | nf1-210 | 17 | 31233030 | 31261794 | + | mRNA | nonsense_mediated_decay |
| -223578 | enst00000583950 | sg00000264538 | suz12p1-207 | 17 | 30784646 | 30790908 | + | lnc_RNA | processed_transcript |
| -223811 | enst00000585268 | sg00000176390 | crlf3-206 | 17 | 30769388 | 30784413 | - | lnc_RNA | processed_transcript |
| -226003 | enst00000585212 | sg00000265791 | ac127024.4-201 | 17 | 30781493 | 30782221 | - | lnc_RNA | lncrna |
| -241721 | enst00000582329 | sg00000264538 | suz12p1-205 | 17 | 30766503 | 30787711 | + | lnc_RNA | processed_transcript |
| 264082 | enst00000584094 | sg00000126861 | omg-204 | 17 | 31272013 | 31273622 | - | lnc_RNA | processed_transcript |
| -270042 | enst00000623719 | sg00000280069 | ac127024.8-201 | 17 | 30738182 | 30740275 | + | unconfirmed_transcript | tec |
| -274161 | enst00000582557 | sg00000264538 | suz12p1-206 | 17 | 30734063 | 30770050 | + | lnc_RNA | processed_transcript |
| -276338 | enst00000578195 | sg00000264538 | suz12p1-203 | 17 | 30731886 | 30776402 | + | pseudogenic_transcript | transcribed_unprocessed_pseudogene |
| -276518 | enst00000497969 | sg00000264538 | suz12p1-201 | 17 | 30731706 | 30758335 | + | lnc_RNA | processed_transcript |
| -278281 | enst00000579639 | sg00000263603 | ac127024.2-202 | 17 | 30729943 | 30731202 | + | lnc_RNA | lncrna |
| -278755 | enst00000581019 | sg00000263603 | ac127024.2-201 | 17 | 30729469 | 30730391 | + | lnc_RNA | lncrna |
| -280660 | enst00000582841 | sg00000265443 | ac127024.3-201 | 17 | 30726305 | 30727564 | - | lnc_RNA | lncrna |
| -283043 | enst00000625101 | sg00000279337 | ac127024.7-201 | 17 | 30724982 | 30725181 | - | unconfirmed_transcript | tec |
| 287690 | enst00000580156 | sg00000126861 | omg-202 | 17 | 31272449 | 31297230 | - | lnc_RNA | processed_transcript |
| 287699 | enst00000247271 | sg00000126861 | omg-201 | 17 | 31294647 | 31297239 | - | mRNA | protein_coding |
| 287999 | enst00000582029 | sg00000126861 | omg-203 | 17 | 31294575 | 31297539 | - | lnc_RNA | retained_intron |
| -298616 | enst00000579526 | sg00000264538 | suz12p1-204 | 17 | 30709608 | 30768876 | + | lnc_RNA | processed_transcript |
| -298925 | enst00000578070 | sg00000264538 | suz12p1-202 | 17 | 30709299 | 30770034 | + | lnc_RNA | processed_transcript |
| 304514 | enst00000330927 | sg00000185862 | evi2b-201 | 17 | 31303770 | 31314054 | - | mRNA | protein_coding |
| 304565 | enst00000577894 | sg00000185862 | evi2b-202 | 17 | 31304234 | 31314105 | - | mRNA | protein_coding |
| -305449 | enst00000483452 | sg00000241631 | rn7sl316p-201 | 17 | 30702504 | 30702775 | - | ncRNA | misc_rna |
| 308873 | enst00000581113 | sg00000196712 | nf1-220 | 17 | 31318413 | 31336473 | + | mRNA | protein_coding |
| 309099 | enst00000581884 | sg00000265118 | ac134669.1-204 | 17 | 31305384 | 31318639 | - | mRNA | nonsense_mediated_decay |
| 309100 | enst00000578021 | sg00000265118 | ac134669.1-202 | 17 | 31305343 | 31318640 | - | mRNA | nonsense_mediated_decay |
| 309100 | enst00000584948 | sg00000265118 | ac134669.1-203 | 17 | 31305356 | 31318640 | - | mRNA | protein_coding |
| 309291 | enst00000578584 | sg00000265118 | ac134669.1-201 | 17 | 31305213 | 31318831 | - | mRNA | protein_coding |
| 311492 | enst00000461237 | sg00000126860 | evi2a-202 | 17 | 31317560 | 31321032 | - | mRNA | protein_coding |
| 312209 | enst00000247270 | sg00000126860 | evi2a-201 | 17 | 31317560 | 31321749 | - | mRNA | protein_coding |
| 312344 | enst00000462804 | sg00000126860 | evi2a-203 | 17 | 31317560 | 31321884 | - | mRNA | protein_coding |
| 320789 | enst00000479536 | sg00000196712 | nf1-209 | 17 | 31330329 | 31336873 | + | mRNA | nonsense_mediated_decay |
| 328223 | enst00000584328 | sg00000196712 | nf1-223 | 17 | 31337763 | 31343098 | + | lnc_RNA | retained_intron |
| 328277 | enst00000471572 | sg00000196712 | nf1-208 | 17 | 31337817 | 31381887 | + | mRNA | nonsense_mediated_decay |
| 328277 | enst00000581790 | sg00000196712 | nf1-221 | 17 | 31337817 | 31360597 | + | mRNA | nonsense_mediated_decay |
| 330740 | enst00000582892 | sg00000196712 | nf1-222 | 17 | 31340280 | 31349150 | + | lnc_RNA | retained_intron |
| 335979 | enst00000581275 | sg00000263535 | ak4p1-201 | 17 | 31345519 | 31346190 | + | pseudogenic_transcript | processed_pseudogene |
| 346264 | enst00000577967 | sg00000196712 | nf1-218 | 17 | 31355804 | 31361602 | + | lnc_RNA | retained_intron |
| 349008 | enst00000468273 | sg00000196712 | nf1-207 | 17 | 31358548 | 31360956 | + | mRNA | protein_coding |
| -362037 | enst00000661384 | sg00000214719 | ac005562.1-209 | 17 | 30646187 | 30665672 | + | lnc_RNA | lncrna |
| -362063 | enst00000652774 | sg00000214719 | ac005562.1-208 | 17 | 30646161 | 30665115 | + | lnc_RNA | lncrna |
| 369108 | enst00000498569 | sg00000196712 | nf1-217 | 17 | 31378648 | 31382116 | + | lnc_RNA | processed_transcript |
| 369351 | enst00000422121 | sg00000196712 | nf1-203 | 17 | 31378891 | 31382106 | + | mRNA | nonsense_mediated_decay |
| 370601 | enst00000488981 | sg00000196712 | nf1-212 | 17 | 31380141 | 31382116 | + | lnc_RNA | processed_transcript |
| -376102 | enst00000417404 | sg00000250462 | lrrc37bp1-203 | 17 | 30632122 | 30637466 | + | lnc_RNA | processed_transcript |
| -376469 | enst00000412831 | sg00000250462 | lrrc37bp1-202 | 17 | 30631755 | 30634170 | + | lnc_RNA | processed_transcript |
| -378544 | enst00000398851 | sg00000250462 | lrrc37bp1-201 | 17 | 30629680 | 30637302 | + | pseudogenic_transcript | transcribed_unprocessed_pseudogene |
| 382135 | enst00000621161 | sg00000131242 | rab11fip4-211 | 17 | 31391675 | 31538211 | + | mRNA | protein_coding |
| 382395 | enst00000581280 | sg00000131242 | rab11fip4-206 | 17 | 31391935 | 31392658 | + | lnc_RNA | processed_transcript |
| -383811 | enst00000582245 | sg00000264943 | sh3gl1p2-201 | 17 | 30624413 | 30625494 | + | pseudogenic_transcript | processed_pseudogene |
| -390434 | enst00000618264 | sg00000273609 | ac005562.2-201 | 17 | 30617680 | 30617790 | - | pseudogenic_transcript | unprocessed_pseudogene |
| -400566 | enst00000440026 | sg00000214719 | ac005562.1-206 | 17 | 30607658 | 30635466 | + | lnc_RNA | lncrna |
| -400578 | enst00000431308 | sg00000214719 | ac005562.1-205 | 17 | 30607646 | 30634162 | + | lnc_RNA | lncrna |
| -400658 | enst00000578265 | sg00000214719 | ac005562.1-204 | 17 | 30607566 | 30672789 | + | lnc_RNA | lncrna |
| -407332 | enst00000651170 | sg00000214719 | ac005562.1-203 | 17 | 30600892 | 30634326 | + | lnc_RNA | lncrna |
| -407359 | enst00000514992 | sg00000248121 | smurf2p1-201 | 17 | 30600865 | 30615980 | + | pseudogenic_transcript | transcribed_unprocessed_pseudogene |
| -407428 | enst00000579301 | sg00000248121 | smurf2p1-202 | 17 | 30600796 | 30615980 | + | lnc_RNA | processed_transcript |
| 422019 | enst00000582009 | sg00000131242 | rab11fip4-208 | 17 | 31431559 | 31521223 | + | mRNA | protein_coding |
| 422273 | enst00000579908 | sg00000131242 | rab11fip4-205 | 17 | 31431813 | 31448495 | + | lnc_RNA | processed_transcript |
| -431224 | enst00000436477 | sg00000231421 | ac011840.1-202 | 17 | 30573471 | 30577000 | - | lnc_RNA | lncrna |
| -431716 | enst00000398849 | sg00000214719 | ac005562.1-202 | 17 | 30576508 | 30634323 | + | lnc_RNA | lncrna |
| -431739 | enst00000667731 | sg00000214719 | ac005562.1-207 | 17 | 30576485 | 30600186 | + | lnc_RNA | lncrna |
| -431760 | enst00000583030 | sg00000214719 | ac005562.1-201 | 17 | 30576464 | 30579682 | + | lnc_RNA | lncrna |
| -433804 | enst00000584763 | sg00000231421 | ac011840.1-203 | 17 | 30573473 | 30574420 | - | lnc_RNA | lncrna |
| -433972 | enst00000582291 | sg00000231421 | ac011840.1-201 | 17 | 30573471 | 30574252 | - | lnc_RNA | retained_intron |
| -436476 | enst00000420566 | sg00000231870 | krt17p3-201 | 17 | 30567700 | 30571748 | - | pseudogenic_transcript | unprocessed_pseudogene |
| -442648 | enst00000563063 | sg00000259928 | ac011840.2-201 | 17 | 30564057 | 30565576 | - | lnc_RNA | lncrna |
| -448658 | enst00000584297 | sg00000266733 | tbc1d29p-204 | 17 | 30559566 | 30563474 | + | lnc_RNA | processed_transcript |
| -448658 | enst00000582511 | sg00000266733 | tbc1d29p-203 | 17 | 30559566 | 30563475 | + | lnc_RNA | retained_intron |
| -448658 | enst00000649411 | sg00000266733 | tbc1d29p-205 | 17 | 30559566 | 30563475 | + | lnc_RNA | processed_transcript |
| -449722 | enst00000582125 | sg00000266775 | ac011840.4-201 | 17 | 30557732 | 30558502 | - | lnc_RNA | lncrna |
| -451112 | enst00000580161 | sg00000266733 | tbc1d29p-202 | 17 | 30557112 | 30563493 | + | lnc_RNA | processed_transcript |
| -454722 | enst00000578471 | sg00000266733 | tbc1d29p-201 | 17 | 30553502 | 30562917 | + | pseudogenic_transcript | transcribed_unprocessed_pseudogene |
| 456003 | enst00000484117 | sg00000239595 | rn7sl79p-201 | 17 | 31465543 | 31465832 | + | ncRNA | misc_rna |
| -457031 | enst00000624536 | sg00000279431 | ac011840.5-201 | 17 | 30551193 | 30551802 | + | unconfirmed_transcript | tec |
| -457035 | enst00000579378 | sg00000263860 | ac011840.3-201 | 17 | 30550493 | 30551189 | - | lnc_RNA | lncrna |
| 478460 | enst00000394744 | sg00000131242 | rab11fip4-201 | 17 | 31488000 | 31531849 | + | mRNA | protein_coding |
| -478536 | enst00000579299 | sg00000264958 | alox12p1-201 | 17 | 30529688 | 30542416 | + | pseudogenic_transcript | unprocessed_pseudogene |
| 478568 | enst00000583755 | sg00000131242 | rab11fip4-209 | 17 | 31488108 | 31525116 | + | mRNA | protein_coding |
| 478578 | enst00000579589 | sg00000131242 | rab11fip4-204 | 17 | 31488118 | 31517708 | + | mRNA | nonsense_mediated_decay |
| 478652 | enst00000578694 | sg00000131242 | rab11fip4-203 | 17 | 31488192 | 31521184 | + | mRNA | nonsense_mediated_decay |
| -488525 | enst00000477885 | sg00000108587 | gosr1-207 | 17 | 30519699 | 30522609 | + | lnc_RNA | retained_intron |
| -497631 | enst00000494918 | sg00000108587 | gosr1-209 | 17 | 30510593 | 30522593 | + | lnc_RNA | retained_intron |
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