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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 |
|---|---|---|---|---|---|---|---|---|
| #41 | 17 | 79814738 | 79816386 | 1648 | 3 | 58 | 9.15521e-23 | 2.2207e-20 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| 2697 | enst00000667764 | sg00000262772 | linc01977-202 | 17 | 79819083 | 79827020 | + | lnc_RNA | lncrna |
| 6248 | enst00000576963 | sg00000262772 | linc01977-201 | 17 | 79822634 | 79827704 | + | lnc_RNA | lncrna |
| -13055 | enst00000485449 | sg00000141570 | cbx8-204 | 17 | 79795394 | 79801683 | - | lnc_RNA | processed_transcript |
| -13205 | enst00000427800 | sg00000141570 | cbx8-203 | 17 | 79795204 | 79801533 | - | mRNA | protein_coding |
| -14140 | enst00000570512 | sg00000262768 | ac100791.2-201 | 17 | 79800598 | 79802529 | + | lnc_RNA | lncrna |
| -16407 | enst00000413392 | sg00000141570 | cbx8-202 | 17 | 79795049 | 79798331 | - | mRNA | protein_coding |
| -17661 | enst00000269385 | sg00000141570 | cbx8-201 | 17 | 79792132 | 79797077 | - | mRNA | protein_coding |
| 21495 | enst00000495122 | sg00000141582 | cbx4-204 | 17 | 79835143 | 79837881 | - | mRNA | protein_coding |
| 23001 | enst00000448310 | sg00000141582 | cbx4-202 | 17 | 79835044 | 79839387 | - | mRNA | protein_coding |
| 23027 | enst00000494546 | sg00000141582 | cbx4-203 | 17 | 79837746 | 79839413 | - | lnc_RNA | retained_intron |
| 23054 | enst00000269397 | sg00000141582 | cbx4-201 | 17 | 79833156 | 79839440 | - | mRNA | protein_coding |
| 33724 | enst00000570408 | sg00000262343 | ac100791.1-201 | 17 | 79848058 | 79850110 | - | lnc_RNA | lncrna |
| -36544 | enst00000269399 | sg00000173894 | cbx2-201 | 17 | 79778194 | 79782532 | + | mRNA | protein_coding |
| -36575 | enst00000571484 | sg00000173894 | cbx2-203 | 17 | 79778163 | 79779739 | + | lnc_RNA | retained_intron |
| -36590 | enst00000310942 | sg00000173894 | cbx2-202 | 17 | 79778148 | 79787983 | + | mRNA | protein_coding |
| -79197 | enst00000576512 | sg00000182156 | enpp7-202 | 17 | 79735541 | 79739568 | + | mRNA | protein_coding |
| -83795 | enst00000328313 | sg00000182156 | enpp7-201 | 17 | 79730943 | 79742219 | + | mRNA | protein_coding |
| 102971 | enst00000574526 | sg00000262188 | linc01978-202 | 17 | 79919357 | 79924010 | + | lnc_RNA | lncrna |
| 102988 | enst00000572353 | sg00000262188 | linc01978-201 | 17 | 79919374 | 79925462 | + | lnc_RNA | lncrna |
| 103029 | enst00000655170 | sg00000262188 | linc01978-203 | 17 | 79919415 | 79925999 | + | lnc_RNA | lncrna |
| -107472 | enst00000592718 | sg00000267719 | linc02078-201 | 17 | 79707266 | 79712317 | + | lnc_RNA | lncrna |
| -107489 | enst00000577633 | sg00000266665 | mir4739-201 | 17 | 79707176 | 79707249 | - | miRNA | mirna |
| 110339 | enst00000576738 | sg00000262585 | linc01979-201 | 17 | 79915252 | 79926725 | - | lnc_RNA | lncrna |
| 134442 | enst00000572862 | sg00000167291 | tbc1d16-205 | 17 | 79943856 | 79950828 | - | mRNA | protein_coding |
| 134444 | enst00000573782 | sg00000167291 | tbc1d16-206 | 17 | 79947648 | 79950830 | - | mRNA | protein_coding |
| 134447 | enst00000574427 | sg00000167291 | tbc1d16-208 | 17 | 79947695 | 79950833 | - | mRNA | protein_coding |
| 134448 | enst00000570373 | sg00000167291 | tbc1d16-203 | 17 | 79944045 | 79950834 | - | mRNA | protein_coding |
| 134450 | enst00000340848 | sg00000167291 | tbc1d16-202 | 17 | 79937908 | 79950836 | - | mRNA | protein_coding |
| 134471 | enst00000576768 | sg00000167291 | tbc1d16-209 | 17 | 79935792 | 79950857 | - | mRNA | protein_coding |
| 135627 | enst00000574241 | sg00000167291 | tbc1d16-207 | 17 | 79947645 | 79952013 | - | mRNA | protein_coding |
| 136277 | enst00000617619 | sg00000275516 | ac100791.3-201 | 17 | 79952663 | 79952992 | + | lnc_RNA | lncrna |
| 176455 | enst00000576632 | sg00000262172 | ac116025.2-201 | 17 | 79991944 | 79992841 | - | lnc_RNA | lncrna |
| 177248 | enst00000571872 | sg00000167291 | tbc1d16-204 | 17 | 79950571 | 79993634 | - | mRNA | protein_coding |
| 207508 | enst00000575404 | sg00000261978 | ac116025.1-201 | 17 | 80023894 | 80026107 | + | lnc_RNA | lncrna |
| 207545 | enst00000570952 | sg00000261978 | ac116025.1-202 | 17 | 80023931 | 80026107 | + | lnc_RNA | lncrna |
| -210817 | enst00000571452 | sg00000263278 | ac233701.1-201 | 17 | 79598032 | 79603921 | - | lnc_RNA | lncrna |
| -213446 | enst00000611949 | sg00000263278 | ac233701.1-202 | 17 | 79598618 | 79601292 | - | lnc_RNA | lncrna |
| 219486 | enst00000310924 | sg00000167291 | tbc1d16-201 | 17 | 79932343 | 80035872 | - | mRNA | protein_coding |
| 220246 | enst00000374877 | sg00000141519 | ccdc40-203 | 17 | 80036632 | 80090819 | + | mRNA | protein_coding |
| 220256 | enst00000397545 | sg00000141519 | ccdc40-204 | 17 | 80036642 | 80100613 | + | mRNA | protein_coding |
| 220266 | enst00000572270 | sg00000141519 | ccdc40-208 | 17 | 80036652 | 80040165 | + | lnc_RNA | processed_transcript |
| 220266 | enst00000269318 | sg00000141519 | ccdc40-201 | 17 | 80036652 | 80067901 | + | mRNA | protein_coding |
| 220272 | enst00000374876 | sg00000141519 | ccdc40-202 | 17 | 80036658 | 80066770 | + | mRNA | protein_coding |
| 220275 | enst00000574099 | sg00000141519 | ccdc40-211 | 17 | 80036661 | 80040187 | + | mRNA | protein_coding |
| 220275 | enst00000576033 | sg00000141519 | ccdc40-215 | 17 | 80036661 | 80040105 | + | mRNA | protein_coding |
| 220278 | enst00000572083 | sg00000141519 | ccdc40-206 | 17 | 80036664 | 80040535 | + | lnc_RNA | retained_intron |
| 220291 | enst00000576241 | sg00000141519 | ccdc40-216 | 17 | 80036677 | 80047454 | + | lnc_RNA | retained_intron |
| 223619 | enst00000573474 | sg00000141519 | ccdc40-209 | 17 | 80040005 | 80050224 | + | mRNA | nonsense_mediated_decay |
| 231984 | enst00000574799 | sg00000141519 | ccdc40-212 | 17 | 80048370 | 80100604 | + | lnc_RNA | retained_intron |
| 242539 | enst00000571028 | sg00000141519 | ccdc40-205 | 17 | 80058925 | 80067288 | + | mRNA | protein_coding |
| 265057 | enst00000572253 | sg00000141519 | ccdc40-207 | 17 | 80081443 | 80097934 | + | lnc_RNA | retained_intron |
| 271128 | enst00000575431 | sg00000141519 | ccdc40-214 | 17 | 80087514 | 80095337 | + | lnc_RNA | retained_intron |
| 271317 | enst00000574933 | sg00000141519 | ccdc40-213 | 17 | 80087703 | 80088212 | + | lnc_RNA | retained_intron |
| 271719 | enst00000573903 | sg00000141519 | ccdc40-210 | 17 | 80088105 | 80092145 | + | lnc_RNA | processed_transcript |
| 282442 | enst00000579691 | sg00000265561 | mir1268b-201 | 17 | 80098828 | 80098877 | + | miRNA | mirna |
| 285170 | enst00000570803 | sg00000171298 | gaa-204 | 17 | 80101556 | 80107718 | + | mRNA | protein_coding |
| 285195 | enst00000302262 | sg00000171298 | gaa-201 | 17 | 80101581 | 80119881 | + | mRNA | protein_coding |
| 285201 | enst00000577106 | sg00000171298 | gaa-209 | 17 | 80101587 | 80105828 | + | mRNA | protein_coding |
| 285208 | enst00000390015 | sg00000171298 | gaa-202 | 17 | 80101594 | 80119877 | + | mRNA | protein_coding |
| 285211 | enst00000574376 | sg00000171298 | gaa-208 | 17 | 80101597 | 80102733 | + | lnc_RNA | processed_transcript |
| 294616 | enst00000572080 | sg00000171298 | gaa-205 | 17 | 80111002 | 80117082 | + | mRNA | nonsense_mediated_decay |
| 295347 | enst00000572803 | sg00000171298 | gaa-206 | 17 | 80111733 | 80112948 | + | lnc_RNA | retained_intron |
| 295998 | enst00000570716 | sg00000171298 | gaa-203 | 17 | 80112384 | 80113271 | + | lnc_RNA | retained_intron |
| -298590 | enst00000580155 | sg00000167281 | rbfox3-203 | 17 | 79090816 | 79516148 | - | mRNA | protein_coding |
| 300440 | enst00000573556 | sg00000171298 | gaa-207 | 17 | 80116826 | 80119275 | + | lnc_RNA | retained_intron |
| -305870 | enst00000584778 | sg00000167281 | rbfox3-212 | 17 | 79094257 | 79508868 | - | mRNA | protein_coding |
| 319936 | enst00000570625 | sg00000141543 | eif4a3-201 | 17 | 80135264 | 80136322 | - | lnc_RNA | retained_intron |
| 321217 | enst00000576573 | sg00000141543 | eif4a3-207 | 17 | 80135264 | 80137603 | - | lnc_RNA | retained_intron |
| 321887 | enst00000575668 | sg00000141543 | eif4a3-203 | 17 | 80136803 | 80138273 | - | lnc_RNA | retained_intron |
| 323101 | enst00000575978 | sg00000141543 | eif4a3-205 | 17 | 80135255 | 80139487 | - | lnc_RNA | retained_intron |
| 324090 | enst00000570837 | sg00000141543 | eif4a3-202 | 17 | 80139686 | 80140476 | - | lnc_RNA | retained_intron |
| 330742 | enst00000649764 | sg00000141543 | eif4a3-209 | 17 | 80134369 | 80147128 | - | mRNA | protein_coding |
| 330753 | enst00000575957 | sg00000141543 | eif4a3-204 | 17 | 80141695 | 80147139 | - | lnc_RNA | retained_intron |
| 330753 | enst00000576547 | sg00000141543 | eif4a3-206 | 17 | 80135349 | 80147139 | - | mRNA | protein_coding |
| 330765 | enst00000647795 | sg00000141543 | eif4a3-208 | 17 | 80135299 | 80147151 | - | mRNA | protein_coding |
| 330864 | enst00000624270 | sg00000279259 | ac087741.3-201 | 17 | 80147250 | 80148596 | + | unconfirmed_transcript | tec |
| -332140 | enst00000583458 | sg00000167281 | rbfox3-211 | 17 | 79089345 | 79482598 | - | mRNA | protein_coding |
| 333241 | enst00000619415 | sg00000275479 | ac087741.2-201 | 17 | 80149627 | 80149798 | + | lnc_RNA | lncrna |
| 353606 | enst00000650867 | sg00000141527 | card14-218 | 17 | 80169992 | 80208971 | + | mRNA | nonsense_mediated_decay |
| 353617 | enst00000573489 | sg00000141527 | card14-207 | 17 | 80170003 | 80179133 | + | lnc_RNA | processed_transcript |
| 353626 | enst00000573882 | sg00000141527 | card14-209 | 17 | 80170012 | 80209331 | + | mRNA | protein_coding |
| 353644 | enst00000648509 | sg00000141527 | card14-215 | 17 | 80170030 | 80209331 | + | mRNA | protein_coding |
| 353648 | enst00000575465 | sg00000141527 | card14-211 | 17 | 80170034 | 80181649 | + | mRNA | protein_coding |
| 353648 | enst00000575500 | sg00000141527 | card14-212 | 17 | 80170034 | 80208963 | + | mRNA | nonsense_mediated_decay |
| 353669 | enst00000651672 | sg00000141527 | card14-221 | 17 | 80170055 | 80209330 | + | mRNA | protein_coding |
| 353677 | enst00000650806 | sg00000141527 | card14-217 | 17 | 80170063 | 80197426 | + | lnc_RNA | retained_intron |
| 353681 | enst00000652599 | sg00000141527 | card14-222 | 17 | 80170067 | 80196343 | + | lnc_RNA | retained_intron |
| 353681 | enst00000651388 | sg00000141527 | card14-220 | 17 | 80170067 | 80202268 | + | mRNA | nonsense_mediated_decay |
| 353891 | enst00000571427 | sg00000141527 | card14-203 | 17 | 80170277 | 80178655 | + | lnc_RNA | processed_transcript |
| 354066 | enst00000651068 | sg00000141527 | card14-219 | 17 | 80170452 | 80208964 | + | mRNA | nonsense_mediated_decay |
| 362113 | enst00000570421 | sg00000141527 | card14-202 | 17 | 80178499 | 80202631 | + | mRNA | protein_coding |
| 362122 | enst00000344227 | sg00000141527 | card14-201 | 17 | 80178508 | 80209309 | + | mRNA | protein_coding |
| 367606 | enst00000648128 | sg00000141527 | card14-214 | 17 | 80183992 | 80192518 | + | mRNA | nonsense_mediated_decay |
| 367765 | enst00000572838 | sg00000141527 | card14-206 | 17 | 80184151 | 80188841 | + | lnc_RNA | retained_intron |
| 367789 | enst00000571450 | sg00000141527 | card14-204 | 17 | 80184175 | 80204235 | + | mRNA | nonsense_mediated_decay |
| 371414 | enst00000573754 | sg00000141527 | card14-208 | 17 | 80187800 | 80198924 | + | lnc_RNA | processed_transcript |
| 371837 | enst00000571861 | sg00000141527 | card14-205 | 17 | 80188223 | 80196030 | + | lnc_RNA | retained_intron |
| 375776 | enst00000574148 | sg00000141527 | card14-210 | 17 | 80192162 | 80198157 | + | lnc_RNA | processed_transcript |
| 375994 | enst00000575666 | sg00000141527 | card14-213 | 17 | 80192380 | 80197532 | + | lnc_RNA | retained_intron |
| 376057 | enst00000649277 | sg00000141527 | card14-216 | 17 | 80192443 | 80208951 | + | lnc_RNA | retained_intron |
| 387949 | enst00000573935 | sg00000262580 | ac087741.1-204 | 17 | 80201746 | 80204335 | - | lnc_RNA | lncrna |
| 388685 | enst00000570309 | sg00000262580 | ac087741.1-201 | 17 | 80200673 | 80205071 | - | lnc_RNA | lncrna |
| 389090 | enst00000573346 | sg00000262580 | ac087741.1-202 | 17 | 80201589 | 80205476 | - | lnc_RNA | lncrna |
| 389241 | enst00000576824 | sg00000262580 | ac087741.1-203 | 17 | 80201708 | 80205627 | - | lnc_RNA | lncrna |
| 389563 | enst00000572730 | sg00000262580 | ac087741.1-205 | 17 | 80203833 | 80205949 | - | lnc_RNA | lncrna |
| -390618 | enst00000578887 | sg00000167281 | rbfox3-201 | 17 | 79233627 | 79424120 | - | lnc_RNA | processed_transcript |
| 393156 | enst00000575484 | sg00000181523 | sgsh-214 | 17 | 80206716 | 80209542 | - | lnc_RNA | processed_transcript |
| 393488 | enst00000571156 | sg00000181523 | sgsh-206 | 17 | 80207605 | 80209874 | - | lnc_RNA | processed_transcript |
| 395832 | enst00000576856 | sg00000181523 | sgsh-216 | 17 | 80210397 | 80212218 | - | mRNA | protein_coding |
| 398336 | enst00000572257 | sg00000181523 | sgsh-209 | 17 | 80207656 | 80214722 | - | mRNA | protein_coding |
| 403313 | enst00000577155 | sg00000181045 | slc26a11-217 | 17 | 80219699 | 80223283 | + | mRNA | protein_coding |
| 403872 | enst00000574505 | sg00000181523 | sgsh-211 | 17 | 80213821 | 80220258 | - | mRNA | nonsense_mediated_decay |
| 403936 | enst00000575282 | sg00000181523 | sgsh-213 | 17 | 80209282 | 80220322 | - | lnc_RNA | retained_intron |
| 403945 | enst00000572208 | sg00000181523 | sgsh-208 | 17 | 80213832 | 80220331 | - | lnc_RNA | processed_transcript |
| 403947 | enst00000326317 | sg00000181523 | sgsh-201 | 17 | 80209276 | 80220333 | - | mRNA | protein_coding |
| 403947 | enst00000576941 | sg00000181523 | sgsh-217 | 17 | 80212205 | 80220333 | - | mRNA | nonsense_mediated_decay |
| 403947 | enst00000571051 | sg00000181523 | sgsh-204 | 17 | 80214166 | 80220333 | - | lnc_RNA | retained_intron |
| 403947 | enst00000571075 | sg00000181523 | sgsh-205 | 17 | 80216723 | 80220333 | - | lnc_RNA | retained_intron |
| 403947 | enst00000570427 | sg00000181523 | sgsh-202 | 17 | 80214290 | 80220333 | - | mRNA | protein_coding |
| 403947 | enst00000571675 | sg00000181523 | sgsh-207 | 17 | 80214570 | 80220333 | - | lnc_RNA | retained_intron |
| 403947 | enst00000575188 | sg00000181523 | sgsh-212 | 17 | 80214855 | 80220333 | - | lnc_RNA | retained_intron |
| 403952 | enst00000570923 | sg00000181523 | sgsh-203 | 17 | 80211534 | 80220338 | - | mRNA | protein_coding |
| 403974 | enst00000573150 | sg00000181523 | sgsh-210 | 17 | 80209290 | 80220360 | - | mRNA | nonsense_mediated_decay |
| 404041 | enst00000573809 | sg00000181045 | slc26a11-213 | 17 | 80220427 | 80223272 | + | mRNA | protein_coding |
| 404041 | enst00000361193 | sg00000181045 | slc26a11-201 | 17 | 80220427 | 80253500 | + | mRNA | protein_coding |
| 404052 | enst00000574967 | sg00000181045 | slc26a11-214 | 17 | 80220438 | 80221793 | + | mRNA | protein_coding |
| 404052 | enst00000572652 | sg00000181045 | slc26a11-211 | 17 | 80220438 | 80222375 | + | lnc_RNA | retained_intron |
| 404052 | enst00000576126 | sg00000181045 | slc26a11-216 | 17 | 80220438 | 80225916 | + | mRNA | protein_coding |
| 404052 | enst00000571888 | sg00000181045 | slc26a11-209 | 17 | 80220438 | 80245373 | + | lnc_RNA | retained_intron |
| 404052 | enst00000411502 | sg00000181045 | slc26a11-202 | 17 | 80220438 | 80253498 | + | mRNA | protein_coding |
| 404052 | enst00000546047 | sg00000181045 | slc26a11-203 | 17 | 80220438 | 80253500 | + | mRNA | protein_coding |
| 404061 | enst00000571602 | sg00000181045 | slc26a11-208 | 17 | 80220447 | 80223255 | + | lnc_RNA | processed_transcript |
| 404083 | enst00000572725 | sg00000181045 | slc26a11-212 | 17 | 80220469 | 80252716 | + | mRNA | protein_coding |
| 404083 | enst00000571564 | sg00000181045 | slc26a11-207 | 17 | 80220469 | 80237103 | + | lnc_RNA | processed_transcript |
| 404537 | enst00000576707 | sg00000181523 | sgsh-215 | 17 | 80214243 | 80220923 | - | mRNA | protein_coding |
| 404914 | enst00000572226 | sg00000181045 | slc26a11-210 | 17 | 80221300 | 80223307 | + | lnc_RNA | processed_transcript |
| 404960 | enst00000571176 | sg00000181045 | slc26a11-205 | 17 | 80221346 | 80227854 | + | mRNA | protein_coding |
| 409196 | enst00000571072 | sg00000181045 | slc26a11-204 | 17 | 80225582 | 80237010 | + | lnc_RNA | retained_intron |
| 411466 | enst00000571215 | sg00000181045 | slc26a11-206 | 17 | 80227852 | 80245245 | + | mRNA | protein_coding |
| 431828 | enst00000575019 | sg00000181045 | slc26a11-215 | 17 | 80248214 | 80252899 | + | mRNA | protein_coding |
| 444480 | enst00000508628 | sg00000173821 | rnf213-204 | 17 | 80260866 | 80395312 | + | mRNA | protein_coding |
| 444482 | enst00000582970 | sg00000173821 | rnf213-220 | 17 | 80260868 | 80398786 | + | mRNA | protein_coding |
| 444484 | enst00000319921 | sg00000173821 | rnf213-201 | 17 | 80260870 | 80321463 | + | mRNA | protein_coding |
| 471573 | enst00000559070 | sg00000173821 | rnf213-207 | 17 | 80287959 | 80336900 | + | lnc_RNA | retained_intron |
| 473375 | enst00000573548 | sg00000173821 | rnf213-216 | 17 | 80289761 | 80292007 | + | lnc_RNA | retained_intron |
| 479343 | enst00000574060 | sg00000173821 | rnf213-218 | 17 | 80295729 | 80298775 | + | lnc_RNA | retained_intron |
| 499265 | enst00000576808 | sg00000262979 | ac124319.1-201 | 17 | 80315651 | 80316633 | + | 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