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Table 2 Genes annotated to the top replicated DARs

From: Genome-wide histone acetylation analysis reveals altered transcriptional regulation in the Parkinson’s disease brain

Symbol Region Annotation CHR Region
Location
Peak
Location (PW, NBB)
MetaP LFC
PW, NBB
PeakName
PW, NBB
Proportion
Significant
Common hypoacetylated regions
PTPRH introns 19 55,718,568–55,720,750 55,720,288–55,722,414, 55,717,912–55,719,103 1.7E-07 −0.81, −0.94 Peak_20188, Peak_15767 3p/4 (0.8)
JUP introns 17 39,681,526–39,923,630 39,805,764–39,808,133, 39,807,092–39,808,006 1.1E-05 −0.43, − 0.99 Peak_53983, Peak_81536 5p/10p (0.5)
Common hyperacetylated regions (top 15)
DLG2a exons 11 83,874,504–83,874,554 83,873,551–83,879,844, 83,873,666–83,877,544 7.7E-12 0.68, 1.05 Peak_21808, Peak_40741 30p/49p(0.6)
KIT exons 4 55,604,595–55,606,881 55,606,747–55,609,274, 55,606,782–55,609,553 8.1E-11 0.63, 1.26 Peak_21777, Peak_37103 2/3p (0.7)
CNTNAP2 exons 7 147,336,198–147,336,398 147,333,973–147,338,260, 147,333,944–147,337,213 6.2E-09 0.51, 1.07 Peak_44999, Peak_47588 11/18p (0.6)
RNF216 introns 7 5,681,008–5,692,043 5,679,685–5,685,127, 5,688,370–5,705,729 1.2E-08 0.6, 0.53 Peak_38631, Peak_12618 11p/16 (0.7)
FRMD5 introns 15 44,216,508–44,393,656 44,260,324–44,263,821, 44,244,249–44,247,825 1.6E-08 0.68, 0.67 Peak_18018, Peak_18744 12p/17p(0.7)
SOX2-OT introns 3 181,328,718–181,417,385 181,358,880–181,360,150, 181,341,154–181,348,014 1.7E-08 0.55, 0.91 Peak_43667, Peak_31549 9/12 (0.8)
MAGI2 1to5kb 7 78,120,338–78,124,337 78,121,257–78,128,843, 78,115,190–78,121,170 2.2E-08 0.4, 0.93 Peak_18816, Peak_24042 9p/23 (0.4)
PPP2R2B introns 5 146,080,706–146,460,621 146,383,635–146,384,203, 146,459,075–146,469,815 2.8E-08 1.3, 0.52 Peak_135972, Peak_17645 17p/27p(0.6)
KCNH1 introns 1 210,948,887–210,970,849 210,966,438–210,969,215, 210,946,491–210,950,181 3.8E-08 0.55, 1.0 Peak_51838, Peak_38212 9/18p (0.5)
CDH1 introns 16 68,835,797–68,842,326 68,840,159–68,841,130, 68,782,065–68,837,136 4.8E-08 0.84, 0.37 Peak_66179, Peak_3389 5/7p (0.7)
MAP 4 K4a introns 2 102,315,001–102,407,181 102,330,963–102,334,475, 102,367,013–102,375,949 5.2E-08 0.54, 0.62 Peak_30093, Peak_9009 10p/24p(0.4)
METTL24 introns 6 110,644,076–110,729,536 110,656,829–110,661,962, 110,685,537–110,688,887 5.4E-08 0.48, 0.97 Peak_22739, Peak_27591 8/13p(0.6)
PIP4K2A introns 10 22,898,647–23,003,111 22,934,570–22,952,399, 22,957,818–22,962,517 5.6E-08 0.58, 0.52 Peak_22480, Peak_27954 9p/18p(0.5)
SIK3 introns 11 116,827,781–116,968,858 116,825,819–116,835,556, 116,846,923–116,884,577 5.8E-08 0.6, 0.49 Peak_21504, Peak_11226 13p/16p(0.8)
DOCK10 introns 2 225,796,386–225,906,968 225,798,681–225,800,264, 225,845,772–225,849,871 8.1E-08 0.61, 0.77 Peak_94440, Peak_22866 6/10p(0.6)
Common hyperacetylated regions (additional GWAS hits)
CRHR1a introns 17 43,707,525–43,750,192 43,726,544–43,728,643, 43,741,886–43,747,152 2.0E-07 0.43, 0.83 Peak_74390, Peak_30944 6/14p(0.4)
MBNL2a introns 13 97,873,814–97,927,885 97,919,075–97,922,481, 97,906,667–97,916,758 1.2E-05 0.44, 0.44 Peak_29656, Peak_16279 14p/22p(0.6)
  1. For hyperacetylated regions, the top 15 genes with DARs common to the two cohorts and common DARs in genes previously associated with PD are shown. The genes were ranked based on Fisher’s meta p-value. The full list of genes is provided in Supplementary Table S6
  2. aPrevious association with PD based on GWAS; Region Location – genomic location (on the indicated chromosome) of the annotated region; Peak location – genomic location of the relevant peak from each cohort (upper – PW, lower - NBB); LFC – log fold change compared to controls; Peak Name – the peak identifier in each cohort; Proportion significance – DARs/total common regions annotated to the gene; p- peaks annotated to promoter region of the gene