Table 2.

H3K4me3 is altered at 78 loci in HD cortical neurons, compared with control neuron

TSS	bp to TSS	Mean CTR	Mean HGT	Log2(CTR/ HGT)	P-value (t-test)	FDR	Functions
ARC	1715	0.0215	0.0097	2.543	0.0031	0.046	Activity-regulated early response gene with key role in synaptic plasticity
BHLHE40	3320	0.0192	0.0077	1.774	0.0013	0.031	A bHLH transcription factor and key component of the circadian clock
TMEM200B	0	0.0050	0.0124	1.618	0.0011	0.029
MIR3675	11662	0.0140	0.0041	1.604	0.0035	0.048
MIR1257	11074	0.0290	0.0140	1.522	0.0004	0.021
FBXL16	2707	0.0106	0.0042	1.515	0.0001	0.014
NR4A1	10907	0.0101	0.0045	1.515	0.0000	0.011	Nuclear receptor-related transcription factor implicated in neuroprotection;
SLC22A18	0	0.0105	0.0040	1.508	0.0003	0.018
DAB2IP	0	0.0111	0.0047	1.448	0.0005	0.023	A GTPase regulator involved in neuronal migration and growth
HBQ1	0	0.0101	0.0035	1.432	0.0001	0.012
PHLDA2	0	0.0176	0.0080	1.420	0.0010	0.028
RNF126	3401	0.0126	0.0051	1.376	0.0028	0.043
BAI1	46840	0.0122	0.0056	1.345	0.0014	0.032	Angiogenesis inhibitor 1, interacts with LRRK2 kinase
CYP2S1	0	0.0184	0.0080	1.333	0.0001	0.014
LOXL4	0	0.0187	0.0087	1.324	0.0022	0.039
MIDN	1136	0.0047	0.0126	1.324	0.0007	0.024	Nucleolar protein with ubiquitin-like domain essential for mid-brain development
KIAA1274	0	0.0133	0.0292	1.321	0.0000	0.003
HES4	0	0.0122	0.0055	1.320	0.0000	0.011	Regulator of neural stem-cell proliferation
FOS	0	0.0325	0.0148	1.320	0.0010	0.029	Early response gene involved in activity-regulated gene expression
RAMP3	0	0.0158	0.0391	1.313	0.0004	0.020
ETV4	0	0.0243	0.0098	1.307	0.0023	0.040
INF2	0	0.0235	0.0105	1.306	0.0001	0.013	Inverted formin, a monogenic risk gene for Charcot–Marie–Tooth neuropathy
VRK1	235498	0.0108	0.0036	1.305	0.0003	0.018	Monogenic causative gene for postnatal progressive microcephaly syndromes
DSG2	0	0.0159	0.0071	1.296	0.0001	0.011
BRSK2	19307	0.0190	0.0083	1.293	0.0014	0.033	BRSK2/SAD defines neuronal polarization and axon growth in cerebral cortex
NPAS4	0	0.0144	0.0059	1.276	0.0017	0.035	An activity-dependent TF critical for memory and inhibitory synape formation
ADRA1D	0	0.0166	0.0074	1.268	0.0023	0.040	Adrenergic receptor 1D, expressed in forebrain
SLC27A5	1597	0.0123	0.0056	1.265	0.0005	0.023
PPIC	0	0.0112	0.0048	1.247	0.0001	0.013
KCNN1	0	0.0188	0.0401	1.237	0.0020	0.037	Calcium-activated potassium channel SK-1, implicated in neuroprotection
GNG13	0	0.0170	0.0391	1.231	0.0017	0.035
AGRN	12379	0.0118	0.0047	1.224	0.0001	0.014	Synaptogenesis and plasticity in CNS, key neuromuscular junction protein
GOLT1A	62360	0.0174	0.0378	1.216	0.0037	0.049
SLC26A1	3435	0.0142	0.0305	1.198	0.0010	0.028
C6orf27	0	0.0145	0.0067	1.196	0.0000	0.011
JAG2	395	0.0124	0.0056	1.192	0.0001	0.013	Notch receptor ligand Jagged 2, implicated in generation of motor neurons.
HHATL	0	0.0181	0.0066	1.190	0.0014	0.032
CLEC2L	0	0.0353	0.0165	1.190	0.0000	0.008
C1orf187	0	0.0139	0.0057	1.179	0.0026	0.042	Neural-specific antagonist to WNT signaling and axon guidance molecule
C19orf26	0	0.0215	0.0075	1.169	0.0010	0.029
CRHR2	0	0.0252	0.0116	1.167	0.0023	0.039	Corticotropin releasing hormone receptor 2
UNC5A	6354	0.0122	0.0272	1.167	0.0016	0.034
FLJ37505	424827	0.0214	0.0092	1.166	0.0000	0.001
AGRN	19672	0.0217	0.0101	1.164	0.0001	0.013	Synaptogenesis and plasticity in CNS, key neuromuscular junction protein
NR4A1	0	0.0110	0.0047	1.163	0.0007	0.026	Nuclear receptor-related transcription factor implicated in neuroprotection
IL2RB	16371	0.0234	0.0094	1.161	0.0034	0.047
KIAA0182	146622	0.0219	0.0494	1.155	0.0005	0.022	Interacting with the disrupted in schizophrenia (DISC1) protein
N4BP3	0	0.0173	0.0068	1.145	0.0000	0.009
TRAF7	2580	0.0126	0.0056	1.144	0.0019	0.037	Encodes TNF receptor-associated protein that regulates apoptosis
MFSD10	0	0.0122	0.0040	1.143	0.0006	0.023
NCR2	91854	0.0147	0.0064	1.139	0.0008	0.026
LOC100128338	0	0.0372	0.0149	1.132	0.0000	0.009
SBK1	30099	0.0111	0.0046	1.132	0.0001	0.014
PDIA6	23739	0.0192	0.0079	1.129	0.0030	0.045	An isomerase interacting with progranulin, involved in frontotemporal dementia
RCOR2	0	0.0102	0.0041	1.127	0.0001	0.012	Rest Co-repressor 2, chromatin regulator in neuronal progenitor
WTIP	0	0.0100	0.0043	1.119	0.0000	0.009
LGI2	0	0.0123	0.0053	1.118	0.0001	0.012
HAGHL	0	0.0119	0.0048	1.115	0.0001	0.012
LINGO3	0	0.0108	0.0041	1.105	0.0031	0.046
GPR3	0	0.0148	0.0060	1.103	0.0001	0.012	Orphan GPCR modulating beta-amyloid and neurodegeneration
LOC150381	0	0.0259	0.0115	1.102	0.0000	0.008
RHBDL1	0	0.0143	0.0064	1.101	0.0010	0.029
NFIX	0	0.0069	0.0153	1.056	0.0012	0.030	Nuclear protein regulating neural progenitor differentiation in hippocampus
GPM6B	0	0.0121	0.0043	−1.081	0.0009	0.028
SCN2A	0	0.0121	0.0053	−1.091	0.0009	0.027	Sodium channel and monogenic neurodevelopmental risk gene
CHRNA1	76396	0.0209	0.0096	−1.092	0.0013	0.031	Nicotonic acetylcholine receptor important for axonal development
FLRT3	0	0.0160	0.0056	−1.101	0.0029	0.044	Repulsive axon guidance cue
PDZRN3	62936	0.0074	0.0209	−1.119	0.0003	0.018
IL1RAPL1	0	0.0163	0.0074	−1.135	0.0009	0.028	IL 1 receptor accessory protein-like 1, a neurodevelopmental risk gene
SPRED2	0	0.0195	0.0033	−1.151	0.0034	0.048
HMGN4	13970	0.0115	0.0048	−1.156	0.0014	0.032
MTRF1	0	0.0176	0.0375	−1.171	0.0009	0.028
COX7B	0	0.0105	0.0039	−1.198	0.0003	0.018
R3HDM1	54329	0.0118	0.0275	−1.223	0.0020	0.037
KRT222	0	0.0124	0.0263	−1.305	0.0020	0.038
SNRPN	382	0.0176	0.0082	−1.322	0.0033	0.047	Small nuclear riboprotein-associated protein N highly expressed in neurons
ANXA1	71133	0.0150	0.0066	−1.431	0.0011	0.030
ARHGAP21	100221	0.0159	0.0073	−1.500	0.0018	0.036