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Table 2 Genomic features of non-redundant tDMRs

From: Generation of a genomic tiling array of the human Major Histocompatibility Complex (MHC) and its application for DNA methylation analysis

  chr6 coordinates (NCBI_35) TSS CTCF H4K20 me1 PolII H3K4 me2 H3K36 me3 H3K4 me3 DnaseI H3K4 me1 CpG island ECR H2AZ repeats % CpG %
1 29823989–29826356   x      x x   x   x 28.63 2.94
2 30000805–30003606     x    x x      12.6 9.28
*3 30228982–30231712              26.44 2.64
*4 30247370–30249040   x      x x   x    4.73 9.1
*5 30565890–30568365    x x   x x       11.95 4.77
6 30721858–30724158        x      x 5.91 10.52
7 30731648–30734384              42.71 2.27
8 30891136–30893651              95.08 5.24
9 31709197–31711626            x   79.93 5.01
*10 31803609–31806450   x      x x    x   0 2.88
11 31841070–31843352            x   0 11.05
12 32020686–32023216            x   18.4 5.61
13 32056738–32058031 x             6.57 3.935
*14 32067481–32068550              0 3.09
*15 32071709–32072864              0 5.61
16 32073608–32074514              0 5.02
17 32074474–32074660              13.67 3.97
*18 32077678–32079121              0 5.35
*19 32081199–32081780              19.53 5.4
20 32088659–32090434              0 3.685
*21 32088718–32090526              0 3.41
*22 32090749–32092076              1.96 4.22
23 32092057–32093147              0 2.38
24 32094350–32095101              100 1.33
25 32098656–32099323              100 3.59
26 32099573–32100214              0 3.875
*27 32104734–32105602              0 5.29
*28 32107212–32107398              0 5.35
29 32109195–32110435              9.995 5.6
*30 32110416–32111859              19.53 5.4
31 32115381–32116535            x   0 7.27
32 32119000–32120024            x   0 7.61
33 32223988–32226638        x    x    4.19 11.09
34 32659407–32660508        x x   x    9 5
35 32817677–32820582              20.44 2.96
36 32836042–32838492              9.42 7.26
37 33192620–33193912   x            32.79 6.5
*38 33372651–33375048    x x x x x x x   x   10.93 8.76
39 33389687–33392295     x    x     x   2.3 7.51
40 29830203–29832660              6.08 7.77
41 29889483–29892066              21.2 4.15
42 29937894–29939594              38.78 2.48
43 30484481–30486798              96.59 1.04
44 30491424–30493923              1.4 2
45 30526624–30528439        x x      3.54 7.33
46 30527803–30529467   x      x       3.54 6.73
47 30534798–30537070              42.42 1.26
48 30881555–30884300              98.55 4.27
49 31092038–31094660              74.72 7.51
50 31270669–31273172   x      x       4.59 2.75
51 31454436–31456982              8.59 5.84
*52 32590480–32591619              44.47 2.11
53 32622631–32625110              91.09 5.97
54 33132309–33134479         x      24.37 1.01
55 33450625–33452501              84.66 2.88
  1. A total number of 55 non-redundant tDMRs were identified. tDMR co-ordinates on chromosome 6 are provided. tDMRs 1–39 are intragenic and 40–55 intergenic. Enrichment of genomic features, including CpG islands, DNAseI sites, TSSs, ECRs, CTCF binding sites, RNA PolII binding sites, histone marks (H4K20me1, H3K4me2, H3K4me3, H3K36me3, H3K4me1) and H2AZ was tested and marked by symbol 'x' if enrichment was statistically significant (P < 0.05). Percent CpG and repeat density were also determined and are shown for each tDMR. tDMRs 14 – 30 (intragenic) and 51 (intergenic) are mapping to the region encoding for C4A and C4B genes. Asterisks indicate the tDMRs that overlap with Affy_U95 expression array probes.