DMR 40909 chr16:661201-661700 (500bp)
| DMR Stats | |
|---|---|
| Position | chr16:661201-661700 (View on UCSC) |
| Width | 500bp |
| Genomic Context | intron |
| Nearest Genes | RAB40C (0bp away) |
| ANODEV p-value | 0.000584424899601 |
| Frequencies | Benign: 1.0 (14.29%), Low: 1.0 (16.67%), High: 8.0 (88.89 %) |
| Frequent? |
Region Count Boxplot
Region Overview
Gene Overlaps
| Dmrid | Gene Symbol | Gene Id | Isoform Id | Isoform Chr | Isoform Start | Isoform End | Isoform Strand | Overlap Bp | Query Overlap Per | Isoform Overlap Per | Noncoding | Promoter Per | Exonintron Per | End Per |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 40909 | RAB40C | 10685 | uc002chq.3 | chr16 | 640077 | 679273 | + | 500 | 100.0 | 0.47 | 0 | 0.0 | E1 (0), I1 (0), E2 (0), I2 (100), E3 (0), I3 (0), E4 (0), I4 (0), E5 (0), I5 (0), E6 (0), I6 (0), E7 (0) | 0.0 |
| 40909 | RAB40C | 10685 | uc002chr.3 | chr16 | 640173 | 679273 | + | 500 | 100.0 | 0.35 | 0 | 0.0 | E1 (0), I1 (100), E2 (0), I2 (0), E3 (0), I3 (0), E4 (0), I4 (0), E5 (0), I5 (0), E6 (0) | 0.0 |
| 40909 | RAB40C | 10685 | uc021szt.1 | chr16 | 639357 | 679273 | + | 500 | 100.0 | 0.39 | 0 | 0.0 | E1 (0), I1 (0), E2 (0), I2 (100), E3 (0), I3 (0), E4 (0), I4 (0), E5 (0), I5 (0), E6 (0), I6 (0), E7 (0) | 0.0 |
| 40909 | RAB40C | 10685 | uc021szu.1 | chr16 | 639669 | 679273 | + | 500 | 100.0 | 0.29 | 0 | 0.0 | E1 (0), I1 (0), E2 (0), I2 (100), E3 (0), I3 (0), E4 (0), I4 (0), E5 (0), I5 (0), E6 (0), I6 (0), E7 (0) | 0.0 |
| 40909 | RAB40C | 10685 | uc021szv.1 | chr16 | 640077 | 679273 | + | 500 | 100.0 | 0.2 | 0 | 0.0 | E1 (0), I1 (0), E2 (0), I2 (100), E3 (0), I3 (0), E4 (0), I4 (0), E5 (0), I5 (0), E6 (0), I6 (0), E7 (0) | 0.0 |
- 5 geness
Feature Overlaps
| Dmrid | Feature Chr | Feature Start | Feature End | Set | Name | Fields |
|---|---|---|---|---|---|---|
| 40909 | chr16 | 660826 | 661415 | wgEncodeRegDnaseClusteredV2 | 70 | score:1000, srow:427652 |
| 40909 | chr16 | 661034 | 661433 | wgEncodeRegTfbsClusteredV3 | MXI1 | score:339, expCount:1, expNums:441, expScores:339, srow:1443574 |
| 40909 | chr16 | 661044 | 661375 | wgEncodeRegTfbsClusteredV3 | STAT3 | score:223, expCount:3, expNums:567,568,569, expScores:205,223,210, srow:1443575 |
| 40909 | chr16 | 661046 | 661385 | wgEncodeRegTfbsClusteredV3 | HDAC2 | score:152, expCount:1, expNums:181, expScores:152, srow:1443576 |
| 40909 | chr16 | 661051 | 661474 | wgEncodeRegTfbsClusteredV3 | CTCF | score:1000, expCount:91, expNums:0,2,5,9,12,14,16,18,20,24,35,37,39,42,44,49,137,174,213,262,290,463,493,595,597,598,601,603,604,605,606,607,609,612,615,618,621,627,628,629,630,631,635,636,638,639,640,641,642,643,644,645,646,648,650,651,652,653,654,655,656,657,658,659,660,661,662,663,664,665,666,667,669,670,671,672,673,674,675,676,677,678,679,680,681,683,685,686,687,688,689, expScores:1000,401,1000,592,864,640,704,592,388,220,168,346,1000,294,839,224,1000,921,183,247,690,496,266,728,469,1000,439,452,547,679,426,407,801,637,377,221,284,862,1000,1000,881,1000,1000,580,462,223,215,266,365,263,300,623,558,316,689,743,373,927,607,361,378,225,553,971,346,429,1000,561,1000,918,661,804,387,114,1000,649,638,359,627,1000,606,843,277,471,118,1000,1000,1000,667,1000,158, srow:1443577 |
| 40909 | chr16 | 661066 | 661441 | wgEncodeRegTfbsClusteredV3 | YY1 | score:566, expCount:3, expNums:119,162,203, expScores:295,566,294, srow:1443578 |
| 40909 | chr16 | 661089 | 661364 | wgEncodeRegTfbsClusteredV3 | EGR1 | score:218, expCount:1, expNums:138, expScores:218, srow:1443579 |
| 40909 | chr16 | 661090 | 661385 | wgEncodeRegTfbsClusteredV3 | BHLHE40 | score:177, expCount:1, expNums:423, expScores:177, srow:1443580 |
| 40909 | chr16 | 661099 | 661442 | wgEncodeRegTfbsClusteredV3 | GABPA | score:298, expCount:1, expNums:140, expScores:298, srow:1443581 |
| 40909 | chr16 | 661119 | 661400 | wgEncodeRegTfbsClusteredV3 | SMC3 | score:255, expCount:2, expNums:313,450, expScores:255,169, srow:1443582 |
| 40909 | chr16 | 661125 | 661390 | wgEncodeRegTfbsClusteredV3 | RAD21 | score:1000, expCount:9, expNums:108,149,193,231,264,310,355,448,466, expScores:299,1000,1000,268,584,161,799,757,334, srow:1443583 |
| 40909 | chr16 | 661127 | 661416 | wgEncodeRegTfbsClusteredV3 | ZNF143 | score:518, expCount:1, expNums:361, expScores:518, srow:1443584 |
| 40909 | chr16 | 661182 | 661351 | wgEncodeRegTfbsClusteredV3 | CTCFL | score:166, expCount:1, expNums:214, expScores:166, srow:1443585 |
| 40909 | chr16 | 661263 | 661279 | tfbsConsSites | V$YY1_01 | score:876, zScore:1.98, srow:1869255 |
| 40909 | chr16 | 660988 | 661438 | oreganno | OREG0023540 | id:OREG0023540, srow:8403 |
| 40909 | chr16 | 661630 | 661643 | phastConsElements100way | lod=14 | score:255, srow:3213430 |
| 40909 | chr16 | 661662 | 661668 | phastConsElements100way | lod=17 | score:274, srow:3213431 |
| 40909 | chr16 | 661694 | 661712 | phastConsElements100way | lod=26 | score:316, srow:3213432 |
| 40909 | chr16 | 661335 | 661335 | gwasCatalog | rs7204439 | pubMedID:22993228, author:Williams FM, pubDate:2012-09-19, journal:Ann Rheum Dis, title:Novel genetic variants associated with lumbar disc degeneration in northern Europeans: a meta-analysis of 4600 subjects., trait:Disc degeneration (lumbar), initSample:4,683 European ancestry individuals, replSample:NR, region:16p13.3, genes:RAB40C, riskAllele:rs7204439-C, riskAlFreq:0.42, pValue:4E-6, pValueDesc:, orOrBeta:.11, ci95:[0.065-0.155] unit increase, platform:Affymetrix & Illumina [2,552,511] (imputed), cnv:N, srow:5857 |
| 40909 | chr16 | 660037 | 662036 | cpgShelf | — | values(x.gr)[overs$srow, ]:13443 |
- 20 featuress
Omics Overlaps
| Dmrid | Omic Set | Data | Plot |
|---|---|---|---|
| 40909 | cellmeth_recounts | PrEC: 53, LNCaP: 18, DU145: 4 |  |
| 40909 | cellmeth_diffreps_PrECvsLNCaP | A=0, B=12, Length=220, Event=Up, log2FC=Inf, padj=0.00157949948552458 |  |
| 40909 | cellmeth_diffreps_PrECvsLNCaP | A=79, B=9, Length=420, Event=Down, log2FC=-3.13, padj=1.53853878359442e-13 |  |
| 40909 | cellmeth_diffreps_PrECvsDU145 | A=79, B=1, Length=460, Event=Down, log2FC=-6.3, padj=0 |  |
| 40909 | cellexp | id=ENSG00000197562, name=RAB40C, PrEC=1266, str=1075, LNCaP=3058, str=1915, DU145=1377, str=938 |  |
| 40909 | tcgaexp | gene=RAB40C, entrez=57799, pos=chr16:639357-679273(+), B=1884, L=2091, M=2225, H=2141 |  |
| 40909 | pubmed | gene=RAB40C, G=6, GP=0, GC=2, GM=0, GPM=0, GCM=0 |  |