DeepVRegulome

462 fine-tuned DNABERT models for regulatory variant effect prediction

DeepVRegulome is an end-to-end framework for predicting the functional impact of small somatic variants in non-coding regulatory regions using fine-tuned DNABERT models. It covers 458 transcription factors and 4 histone modifications from ENCODE ChIP-seq data.

📄 Paper: arXiv:2511.09026 💻 Code: GitHub 🌐 Web App: deepvregulome.streamlit.app

Quick Start

from transformers import AutoModelForSequenceClassification, AutoTokenizer
import torch

# Load any model using subfolder
model_name = "CTCFL"  # or "SP1", "MYC", "H3K27ac", etc.
tokenizer = AutoTokenizer.from_pretrained(
    "duttaprat/DeepVRegulome", subfolder=f"models/{model_name}"
)
model = AutoModelForSequenceClassification.from_pretrained(
    "duttaprat/DeepVRegulome", subfolder=f"models/{model_name}"
)
model.eval()

# Convert DNA to 6-mer representation
def to_kmer(seq, k=6):
    return " ".join([seq[i:i+k] for i in range(len(seq) - k + 1)])

# Predict binding probability
sequence = "ATCGATCG..."  # 301bp DNA sequence
inputs = tokenizer(to_kmer(sequence), return_tensors="pt",
                   max_length=512, truncation=True, padding=True)
with torch.no_grad():
    prob = torch.softmax(model(**inputs).logits, dim=-1)[0][1].item()
print(f"{model_name} binding probability: {prob:.4f}")

Variant Effect Scoring

import math

def score_variant(model, tokenizer, ref_seq, alt_seq):
    probs = {}
    for name, seq in [("REF", ref_seq), ("ALT", alt_seq)]:
        inputs = tokenizer(to_kmer(seq), return_tensors="pt",
                           max_length=512, truncation=True, padding=True)
        with torch.no_grad():
            probs[name] = torch.softmax(model(**inputs).logits, dim=-1)[0][1].item()

    eps = 1e-7
    lo_ref = math.log((probs["REF"] + eps) / (1 - probs["REF"] + eps))
    lo_alt = math.log((probs["ALT"] + eps) / (1 - probs["ALT"] + eps))
    return {
        "prob_ref": probs["REF"],
        "prob_alt": probs["ALT"],
        "log_odds_change": lo_alt - lo_ref,
        "disrupted": abs(lo_alt - lo_ref) > 2.0,
    }

Available Models (462)

Each model is in models/<NAME>/ subfolder. Load with:

AutoModel.from_pretrained("duttaprat/DeepVRegulome", subfolder="models/<NAME>")

#	Model	Type	Accuracy	F1	ROC-AUC	PR-AUC	Peaks
1	CTCFL	TF	98.39	98.4	99.71	99.7	12743
2	ZNF426	TF	97.09	96.64	98.08	98.65	7915
3	SAFB	TF	97.02	96.81	98.38	98.57	5361
4	RBM34	TF	97	96.53	98.18	98.44	928
5	TAF15	TF	96.74	96.41	99.02	98.58	17900
6	PCBP1	TF	96.7	95.94	99.19	98.66	16229
7	SRSF3	TF	96.6	96.52	98.2	95.53	1610
8	RBM14	TF	96.57	95.73	98.8	98.4	2463
9	KDM4A	TF	96.07	95.99	99.08	98.72	25968
10	NFYA	TF	95.91	95.19	96.88	93.73	4313
11	SPI1	TF	95.79	95.78	98.75	98.38	104150
12	HLF	TF	95.71	95.83	98.88	98.74	66792
13	EGR2	TF	95.68	99.22	99.75	99.6	57610
14	HNRNPLL	TF	95.43	93.73	98.77	97.88	25270
15	HNRNPK	TF	95.41	94.27	97.05	96.06	24014
16	FIP1L1	TF	95.35	94.16	98.25	98.13	10123
17	ZNF654	TF	95.31	95.28	97.93	98.17	33357
18	ZNF146	TF	95.23	94.66	97.57	97.69	38167
19	E2F6	TF	95.14	93.71	98.25	96.91	30723
20	C11orf30	TF	95.13	94.98	98.63	98.61	58686
21	FUS	TF	95.03	93.76	94.87	93.76	7495
22	USF1	TF	94.95	94.93	98.05	97.78	60863
23	ZNF770	TF	94.91	95.01	98.04	97.28	57572
24	AGO1	TF	94.81	92.98	97.19	96.16	16201
25	MAFG	TF	94.74	94.7	97.91	97.78	44030
26	ZFHX2	TF	94.73	99.21	99.82	99.74	61052
27	THAP1	TF	94.7	94.48	98.22	97.82	5210
28	HES2	TF	94.55	84.34	97.15	84.39	6520
29	SRSF1	TF	94.49	93.59	98.34	97.9	9933
30	NFE2	TF	94.22	99.19	99.76	99.72	53717
31	MITF	TF	94.14	93.57	98.35	98.12	36171
32	MAFF	TF	93.91	93.91	97.86	97.17	65684
33	PCBP2	TF	93.89	93.23	96.53	96.61	5328
34	ZIC2	TF	93.77	93.9	97.82	96.94	56766
35	GLIS2	TF	93.74	93.14	98.22	97.8	33566
36	ZNF121	TF	93.64	98.86	99.34	99.26	35805
37	SP2	TF	93.6	93.13	96.81	95.36	27956
38	SCRT2	TF	93.59	98.97	99.56	99.17	59462
39	BATF	TF	93.58	93.82	98.16	97.93	36658
40	HNRNPL	TF	93.57	92.29	97.59	96.88	24447
41	NFE2L2	TF	93.53	91.27	97.24	96.09	26392
42	ZNF585B	TF	93.43	93.4	97.78	98	7381
43	NFYB	TF	93.31	91.7	96.3	95.22	14696
44	ZSCAN4	TF	93.25	92.72	97.64	97.75	23997
45	ZNF316	TF	93.22	93.43	97.42	97.55	97518
46	ZNF140	TF	93.19	92.79	96.45	96.93	7623
47	ZNF777	TF	93.12	92.58	97.24	97.07	7181
48	CBFA2T2	TF	93.06	93.09	97.31	97.25	32239
49	TFAP4	TF	93	92.84	96.79	94.97	27035
50	ATF4	TF	93	92.84	97.72	97.64	39441
51	CTBP2	TF	92.98	92.36	96.78	94.11	7351
52	MXD3	TF	92.88	92.08	98.24	97.87	14677
53	E2F1	TF	92.88	86.4	95.25	91.61	18927
54	ZNF202	TF	92.87	92.87	96.29	96.5	6476
55	ZNF266	TF	92.84	92.56	96.93	96.93	5097
56	ZNF263	TF	92.83	91.44	97.39	96.16	35011
57	ZNF433	TF	92.77	92.49	96.97	97.7	3530
58	RBM39	TF	92.73	91.61	97.44	96.77	29478
59	ZNF680	TF	92.69	92.24	97.36	97.68	10483
60	ZNF341	TF	92.66	92.24	97.24	96.26	33413
61	E2F4	TF	92.64	90.76	97.32	97.07	11270
62	CBFA2T3	TF	92.59	92.67	96.97	96.03	51994
63	ZNF555	TF	92.57	92.23	94.78	96.56	6664
64	RBM25	TF	92.56	92.48	96.96	97.05	47193
65	MAFK	TF	92.55	92.65	97.36	97.6	121216
66	ZNF623	TF	92.53	92.19	96.77	97.51	14353
67	KAT2A	TF	92.45	91.3	92.39	92.84	171
68	SIN3B	TF	92.45	90.29	97.21	96.89	11700
69	CEBPA	TF	92.39	98.89	99.7	99.6	57842
70	U2AF2	TF	92.37	91.72	96.2	94.8	2777
71	ZBTB10	TF	92.27	91.31	96.02	94.41	15441
72	PBX3	TF	92.25	92.23	96.51	95.35	12981
73	SAP30	TF	92.08	90.13	96.21	92.3	15727
74	PHF8	TF	92.03	88.66	96.25	95.67	30275
75	PAX5	TF	92.02	90.77	96.81	94.42	36090
76	ZNF785	TF	92.01	91.35	97.35	97.16	6605
77	ZNF76	TF	92	90.95	93.83	89.14	11676
78	HNF4G	TF	91.93	90.87	96.43	95.82	35204
79	AHR	TF	91.82	91.39	97.21	96.43	10611
80	ZC3H11A	TF	91.8	91.33	96.31	97.12	9905
81	RFX1	TF	91.79	90.4	96.44	96.43	38873
82	SMAD4	TF	91.75	91.7	96.19	94.92	43342
83	UBTF	TF	91.73	89.06	94.72	91.45	19173
84	ZNF704	TF	91.71	90.84	94.66	94.52	1834
85	TAL1	TF	91.69	90.15	96.07	95.03	36574
86	ZBTB7A	TF	91.69	90.22	97.14	95.99	37497
87	CEBPB	TF	91.69	98.47	99.54	99.42	148540
88	NFIL3	TF	91.67	91.52	96.42	96	38852
89	XRCC5	TF	91.61	90.04	95.9	93.22	32847
90	U2AF1	TF	91.6	89.92	96.08	96	8379
91	ZNF34	TF	91.58	91.34	95.28	96.71	9650
92	FOXP2	TF	91.57	90.78	96.14	93.84	24150
93	AGO2	TF	91.55	89.26	95.16	94.66	33079
94	RUNX3	TF	91.53	98.64	99.5	99.27	69903
95	ZBED5	TF	91.49	91.43	97.14	96.94	5100
96	RARA	TF	91.46	91.59	95.97	94.89	42489
97	FOS	TF	91.45	98.69	99.62	99.63	169317
98	SP3	TF	91.44	90.22	95.27	94.77	23619
99	NANOG	TF	91.43	90.45	95.72	94.36	15681
100	USF2	TF	91.39	89.66	96.88	96.27	37240
101	SP5	TF	91.37	91.12	95.54	94.28	23155
102	HNF4A	TF	91.37	91.63	96.12	95.11	89892
103	ZNF354C	TF	91.37	90.59	95.08	96.39	1640
104	ZNF444	TF	91.35	90.8	95.64	94.38	25366
105	GMEB2	TF	91.33	90.21	95.76	95.89	4800
106	ZNF677	TF	91.33	91.35	94.68	94.52	5777
107	IRF4	TF	91.18	91.14	96.12	95.26	21810
108	ETV5	TF	91.18	90.89	96.55	95.11	29604
109	PRPF4	TF	91.14	89.78	96.21	95.93	8605
110	FOXA3	TF	91.12	91.46	96.8	96.6	45297
111	ZNF292	TF	91.11	90.59	94.63	96.11	1900
112	GLIS1	TF	91.07	90.1	96.04	95.32	58506
113	FOXA2	TF	91.05	91.28	96.39	96.06	99343
114	KLF9	TF	90.99	87.95	95.59	94.68	32290
115	SOX5	TF	90.98	90.85	95.23	93.77	37979
116	BCL6	TF	90.97	90.9	96.3	95.48	38142
117	IRF3	TF	90.97	87.65	96.01	95.01	5726
118	ZNF223	TF	90.97	90.6	95.52	95.63	5176
119	HCFC1	TF	90.96	85.32	94.4	91.32	19700
120	HNRNPH1	TF	90.85	89.75	96.02	95.65	2446
121	DEAF1	TF	90.85	90.18	94.68	95.53	3170
122	CEBPZ	TF	90.82	86.79	89.86	85.64	1971
123	PTBP1	TF	90.8	89.88	94.48	89.35	8063
124	STAT3	TF	90.79	90.81	96.82	96.85	65231
125	KAT2B	TF	90.77	90.48	96.6	96.8	3106
126	SOX13	TF	90.76	90.83	96.32	95.69	48796
127	ZNF423	TF	90.75	90.32	94.63	93.05	11299
128	STAT2	TF	90.73	89.46	95.84	93.72	4303
129	MEIS2	TF	90.71	90.78	96.27	96.07	52199
130	ATF2	TF	90.69	90.57	94.77	94.25	110897
131	NFIA	TF	90.67	90.58	95.6	95.07	27816
132	PATZ1	TF	90.67	89.53	96.62	95.93	35416
133	ZNF398	TF	90.66	89.94	94.96	92.96	26224
134	KLF1	TF	90.65	89.32	94.52	92.79	40024
135	SCRT1	TF	90.65	90.42	94.93	94.54	25487
136	NFIB	TF	90.65	87.93	96.05	95.1	27982
137	PLRG1	TF	90.64	90.06	96.68	96.85	2256
138	PRDM1	TF	90.62	95.17	98.83	98.73	50489
139	ZNF133	TF	90.61	90.22	95.36	94.71	8423
140	SREBF2	TF	90.59	89.11	96.2	95.55	4933
141	EBF1	TF	90.59	90.64	95.31	94.3	56947
142	THAP11	TF	90.57	89.79	94.85	93.4	31698
143	ZNF48	TF	90.56	89.58	94.31	91	28840
144	POU5F1	TF	90.56	89.71	96.35	95.35	7870
145	RB1	TF	90.5	87.95	94	91.78	31314
146	ZBTB6	TF	90.44	90.06	95.43	95.01	13955
147	HNF1A	TF	90.44	90.13	93.47	91.12	12818
148	KDM5B	TF	90.43	88.75	96.53	95.91	18356
149	ZNF521	TF	90.37	90.04	96.17	96.82	1585
150	GLI4	TF	90.37	90.04	96.45	96.57	6130
151	RERE	TF	90.37	89.28	95.15	93.11	11849
152	ZBTB26	TF	90.33	87.38	93.76	90.92	32837
153	FOXP1	TF	90.33	89.44	95.14	93.99	31380
154	ZNF596	TF	90.31	89.88	95.56	95.65	14087
155	ZBTB21	TF	90.29	89.52	96.14	95.86	18547
156	HMGXB4	TF	90.27	89.5	93.94	91.67	25984
157	TEAD1	TF	90.27	90.29	95.53	94.84	33326
158	ZNF660	TF	90.18	89.77	94.75	94.22	29821
159	SFPQ	TF	90.18	90.09	91.7	90.66	335
160	ZNF658	TF	90.14	88.6	93.92	94.54	1325
161	SKI	TF	90.12	89.27	95.47	93.65	30460
162	SRF	TF	90.12	87.92	96	94.95	27692
163	CEBPG	TF	90.11	90.14	96.25	96.42	87912
164	ZHX1	TF	90.1	88.61	94.55	92.57	5512
165	RUNX1	TF	90.07	89.3	94.29	91.85	7554
166	RXRB	TF	90.07	89.83	94.62	92.92	38236
167	ZBTB48	TF	90.05	89.29	96.26	95.22	24899
168	ZNF747	TF	90.02	88.84	95.87	95.94	1427
169	VEZF1	TF	90.01	88.14	94.32	93.48	35726
170	GATA1	TF	89.96	87.31	93.39	91.08	33326
171	ZNF670	TF	89.95	88.3	95.12	95.63	1288
172	ARID4B	TF	89.94	88.99	94.05	92.27	42648
173	ZNF449	TF	89.94	89.32	94.61	94.5	18374
174	KLF17	TF	89.93	89.05	96.18	95.48	25375
175	ZBTB20	TF	89.91	88.23	95.2	92.94	31889
176	ELF3	TF	89.85	89.43	95.06	93.86	35966
177	ZNF16	TF	89.85	89.14	95.41	95.27	2784
178	ZMIZ1	TF	89.85	90.09	95.22	95.28	1077
179	ZSCAN5A	TF	89.84	89.2	93.59	90.92	8202
180	ZNF143	TF	89.84	98.49	99.48	99.5	66295
181	ZNF513	TF	89.78	88.85	94.49	95.41	11211
182	PPARG	TF	89.77	89.47	94.59	93.53	23903
183	ZBTB8A	TF	89.73	88.24	94	92.72	32420
184	IRF5	TF	89.71	89.41	93.56	94.62	2755
185	ZMYM3	TF	89.71	89.32	95.52	95.45	43157
186	DEK	TF	89.7	88.82	95.38	93.29	8490
187	GABPB1	TF	89.7	89.12	94.29	92.92	47437
188	ZNF629	TF	89.69	88.91	94.14	92.43	37813
189	ETV1	TF	89.68	89.39	95.3	95.09	20672
190	ZNF394	TF	89.67	88.63	94.54	94.01	28297
191	TEAD4	TF	89.66	89.49	95.4	94.56	34189
192	PHF20	TF	89.63	88.59	94.4	91.57	13930
193	RBBP5	TF	89.59	85.4	96.01	94.46	30322
194	NFYC	TF	89.59	89.07	95.3	95.46	15080
195	ELK1	TF	89.58	84.66	91.33	89.55	12298
196	H4K12ac	HISTONE	89.57	89.53	96.1	95.46	42837
197	HMBOX1	TF	89.55	88.79	95.65	94.82	24883
198	KDM5A	TF	89.53	82.52	92.86	90.18	13023
199	WHSC1	TF	89.51	89.25	94.42	89.89	1801
200	ZNF692	TF	89.51	88.62	94.15	92.63	30183
201	MEF2B	TF	89.51	88.5	94.65	93.45	34822
202	TCF7L2	TF	89.46	86.81	94.06	91.99	28567
203	SAP130	TF	89.46	89.63	93.52	92.26	58021
204	SETDB1	TF	89.45	87.69	96.29	95.41	4903
205	ZKSCAN1	TF	89.45	87.61	94.37	92.44	20226
206	GATA4	TF	89.43	88.99	94.52	91.79	12156
207	EGR1	TF	89.43	89.26	93.84	93.58	67451
208	SUZ12	TF	89.36	82.88	94.21	91.33	24316
209	HDAC6	TF	89.35	87.38	95.07	94.75	5762
210	TEAD3	TF	89.35	89.2	95.32	93.94	42854
211	SRSF9	TF	89.34	87.07	96.1	95.7	846
212	MLX	TF	89.33	88.85	93.58	91.33	14640
213	ARID1B	TF	89.32	88.77	95.17	94.59	45992
214	ZSCAN30	TF	89.31	88.65	94.12	92.49	24704
215	ZFP36	TF	89.3	86.44	94.32	92.7	32993
216	ZFP64	TF	89.3	88.8	94.25	93.12	9433
217	ZNF518A	TF	89.3	88.1	94.68	95.04	16690
218	ZNF512	TF	89.29	87.52	95.55	95.6	17500
219	MEF2C	TF	89.25	89.19	94.66	93.88	11421
220	ARID2	TF	89.24	88.78	93.47	91.82	11585
221	IKZF5	TF	89.21	88.59	94.7	92.99	25386
222	PRDM2	TF	89.19	88.58	93.29	91.23	3824
223	KDM6A	TF	89.17	88.82	95.31	94.56	12193
224	RXRA	TF	89.17	89.44	94.78	93.82	85611
225	NRF1	TF	89.15	87.63	93.52	92.27	41391
226	MEF2A	TF	89.15	89.07	95.08	95.07	22725
227	SREBF1	TF	89.15	87.65	95.62	95.11	13518
228	BCOR	TF	89.08	88.74	95.34	94.44	41985
229	FOSL1	TF	89.06	88.05	94.11	93.96	43596
230	ZFP69B	TF	89.05	88.39	94.54	93.79	21782
231	ZNF837	TF	89	88.53	94.06	94.52	2332
232	CREB1	TF	88.96	89.04	95.48	96.05	89914
233	KDM3A	TF	88.94	88.07	92.68	88.4	15970
234	POU2F2	TF	88.92	88.77	93.25	89.71	19963
235	RBPJ	TF	88.92	87.6	94.85	93.61	24864
236	H2AK9ac	HISTONE	88.91	89.24	94.58	92.7	129243
237	IRF2	TF	88.9	87.49	93.77	92.14	31753
238	EED	TF	88.9	88.18	94.22	92.87	33175
239	CBFB	TF	88.89	87.72	93.81	91.26	18476
240	ZNF362	TF	88.88	87.44	94.25	92.46	20426
241	HMG20A	TF	88.87	88.31	94.68	93.45	24288
242	NR2F6	TF	88.87	88.87	93.72	92	59262
243	MIXL1	TF	88.8	88.4	94.17	93.38	25659
244	ZNF768	TF	88.79	88.37	92.77	94.22	7605
245	ZNF791	TF	88.77	87.99	94.79	95.45	3900
246	ZNF652	TF	88.76	88.46	95.01	94.59	15412
247	GTF2B	TF	88.76	86.89	94.01	94.5	1890
248	CBX1	TF	88.75	87.21	94.69	92.62	12838
249	KLF4	TF	88.72	86.04	92.03	91.82	6883
250	HHEX	TF	88.7	88.36	95.48	94.32	7808
251	ZFP91	TF	88.7	87.92	93.44	93.1	12862
252	ETS1	TF	88.69	84.7	94.07	90.02	30554
253	FOSL2	TF	88.66	88.52	92.87	91.8	54934
254	GMEB1	TF	88.61	86.89	94.78	94.21	22958
255	MYRF	TF	88.61	88.08	92.66	88.81	6038
256	CREB3L1	TF	88.6	86.11	93.55	91.45	16274
257	MBD2	TF	88.6	85.96	94.29	92.38	20596
258	ZNF384	TF	88.58	88.42	94.86	94.74	49451
259	ZNF664	TF	88.58	88.58	94.23	93.8	26774
260	SP7	TF	88.58	87.43	93.73	92.33	43425
261	AEBP2	TF	88.57	88.27	92.65	93.95	2439
262	HOMEZ	TF	88.57	88.43	94.49	93.05	25047
263	ZNF514	TF	88.55	88.75	93.62	94.15	1637
264	DRAP1	TF	88.55	87.7	93.04	91.43	23241
265	HSF1	TF	88.53	86.77	93.77	93.41	3588
266	FOXA1	TF	88.52	88.77	94.82	94.45	144475
267	KLF10	TF	88.52	87.13	93.65	91.19	18933
268	ZNF18	TF	88.49	87.85	93.25	92.44	18879
269	GATAD1	TF	88.45	87.54	92.76	90.62	22354
270	BRCA1	TF	88.43	84.43	91.88	90.63	4271
271	GATA3	TF	88.41	88.76	93.95	93.68	89323
272	TBX3	TF	88.37	86.69	92.33	87.32	16097
273	HIC1	TF	88.34	87.87	95.07	94.7	24393
274	ELF4	TF	88.29	85.91	91.81	90.4	19552
275	KLF7	TF	88.28	87.47	95.07	95.1	11741
276	MAZ	TF	88.25	88.01	93.3	92.34	57653
277	YY2	TF	88.25	87.53	94.5	93.99	9753
278	RLF	TF	88.25	87.22	91.97	89.17	9482
279	ZNF561	TF	88.25	87.47	92.52	89.34	21469
280	HBP1	TF	88.25	87.02	94.35	92.31	13101
281	PBX2	TF	88.24	86.87	92.57	90.17	38883
282	GATA2	TF	88.17	88.14	93.72	92.79	71662
283	ESRRA	TF	88.17	86.95	93.13	89.98	41619
284	ZNF189	TF	88.17	87.09	93.99	92.74	35323
285	MIER2	TF	88.16	87.72	93.74	92.28	15598
286	TBX21	TF	88.15	87.4	94.73	94.2	38025
287	DMAP1	TF	88.15	86.04	92.88	89.99	21794
288	RFX3	TF	88.14	87.7	92.23	93.25	6180
289	FEZF1	TF	88.12	87.4	94.8	93.99	31350
290	ZNF248	TF	88.12	87.31	92.8	92.85	2499
291	ZNF600	TF	88.11	87.42	93.97	90.88	45001
292	NR2F2	TF	88.09	88	95.03	94.56	55514
293	ZNF560	TF	88.07	87.67	95.15	96.12	3447
294	BHLHE40	TF	88.01	88	92.37	91.72	90623
295	NFKBIZ	TF	88	86.89	93.2	90.86	12731
296	SOX6	TF	87.97	87.18	92.97	91.69	36530
297	NCOA1	TF	87.95	83.89	92.56	89.24	26193
298	ZNF2	TF	87.94	86.44	92.68	91	24945
299	JUNB	TF	87.93	88.02	92.72	91.19	51972
300	KDM4B	TF	87.93	86.42	93.56	94.18	7803
301	ZNF10	TF	87.88	87.16	93.83	93.93	17922
302	MYB	TF	87.86	86.65	94.72	93.1	3337
303	MGA	TF	87.84	86.5	91.45	85.5	28338
304	ZBTB2	TF	87.82	86.59	94.58	94.15	16341
305	ZEB1	TF	87.82	85.07	94.37	93.15	20733
306	REPIN1	TF	87.81	86.18	94.22	94.58	5721
307	ZNF148	TF	87.79	85.69	92.13	92.12	21902
308	ERF	TF	87.78	86.48	92.92	90.58	27611
309	KLF8	TF	87.78	86.2	91.63	88.66	27450
310	MYC	TF	87.77	87.53	93.73	92.94	94483
311	TRIM22	TF	87.77	97.99	99.03	99.13	55932
312	RFX5	TF	87.76	81.96	92.33	89.55	24728
313	DACH1	TF	87.72	87.31	92.88	92.63	18904
314	ZNF239	TF	87.71	86.87	92.62	91.05	4689
315	ZNF366	TF	87.69	97.9	99.1	98.73	44505
316	PRDM6	TF	87.65	87.25	94.46	92.98	42954
317	ATF3	TF	87.61	87.36	92.96	92.73	94190
318	RAD51	TF	87.58	84.45	93.59	92.92	36133
319	PRDM4	TF	87.55	87.06	93.45	92.04	20853
320	KAT8	TF	87.54	85.89	92.39	89.64	31059
321	MBD1	TF	87.54	84.57	92.74	88.6	18264
322	PKNOX1	TF	87.54	87.54	94.59	94.36	113107
323	WT1	TF	87.54	86.69	92.85	89.27	26226
324	CHD2	TF	87.52	86.08	93.75	91.52	41627
325	ZXDB	TF	87.51	86.1	91.92	88.84	30796
326	HMG20B	TF	87.5	86.97	93.22	90.82	12656
327	SIX5	TF	87.49	79.23	89.33	86.03	10595
328	MAX	TF	87.44	87.59	92.05	89.23	94496
329	TRIM24	TF	87.42	84.62	93.51	90.72	35639
330	NONO	TF	87.4	82.54	89.28	84.68	29192
331	NFE2L1	TF	87.36	83.51	90.34	91.43	10261
332	ZSCAN16	TF	87.36	87.06	92.03	89.65	6915
333	ZNF391	TF	87.36	86.05	92.69	90.97	12610
334	GATAD2A	TF	87.27	87.34	92.84	92.14	59253
335	ZNF282	TF	87.23	85.73	92.1	90.4	12994
336	SMC3	TF	87.23	86.92	93.67	94.33	89498
337	SMARCA4	TF	87.23	87.23	92.59	91.47	94655
338	ZNF645	TF	87.19	85.99	93.82	93.71	3597
339	SIRT6	TF	87.18	86.27	91.81	89.63	831
340	ZNF205	TF	87.17	85.68	93.89	92.45	17444
341	ZBTB11	TF	87.17	83.11	93.24	92.37	34307
342	KLF13	TF	87.15	86.93	90.16	85.26	11590
343	NKRF	TF	87.15	82.95	93.67	92.25	27626
344	OSR2	TF	87.15	86.49	92.7	90.29	33243
345	CC2D1A	TF	87.14	86.24	92.24	91.48	24056
346	NFIC	TF	87.14	87.09	92.88	93.61	74803
347	ZNF138	TF	87.12	86.79	93.04	94.92	1611
348	PHB2	TF	87.11	86.36	93.7	93.49	8362
349	ZHX2	TF	87.11	84.59	92.57	90.95	14751
350	ZNF614	TF	87.09	86.34	92.96	90.43	21841
351	ZBTB44	TF	87.09	86.97	91.7	89.35	19961
352	ZNF501	TF	87.07	84.58	89.56	85.25	18650
353	ZNF547	TF	87.07	87.18	93.08	93.55	4777
354	E4F1	TF	87.05	83.51	91.86	88.4	27783
355	ZNF530	TF	87	86.21	92.54	93.54	2193
356	MYNN	TF	86.97	85.32	92.29	90.37	19348
357	INSM2	TF	86.94	86.19	92.8	91.74	16385
358	ZBTB7B	TF	86.94	85.85	93.93	93.22	9156
359	BCL11B	TF	86.93	86.01	92.01	89.38	11525
360	ZBTB12	TF	86.93	86.23	92.9	91.71	10363
361	PML	TF	86.92	85.32	93.87	93.51	18068
362	SALL2	TF	86.9	86.55	93.23	94.22	2489
363	NR2F1	TF	86.87	86.87	93.08	92.05	70026
364	LCORL	TF	86.86	86.86	93.26	93.83	10617
365	THRB	TF	86.86	86.05	92.7	91.63	14895
366	ZGPAT	TF	86.84	85.13	90.76	86.79	33522
367	MIER3	TF	86.83	85.69	92.53	91.2	19565
368	KMT2B	TF	86.81	84.82	92.77	91.54	17871
369	TGIF2	TF	86.8	85.45	92.88	90.99	18162
370	IKZF2	TF	86.79	86.64	92.67	91.71	52015
371	ZBTB33	TF	86.78	92.02	97.16	96.92	96111
372	NEUROD1	TF	86.73	85.61	92.99	91.71	19165
373	ATF7	TF	86.72	86.65	92.77	93.41	105695
374	SMARCE1	TF	86.71	86.36	92.37	91.4	48505
375	RELB	TF	86.71	84.55	93.6	91.95	36669
376	ELF1	TF	86.71	86.32	93.8	94.5	70684
377	ZNF843	TF	86.68	85.41	92.05	89.55	22911
378	ATM	TF	86.67	85.99	93.74	94.31	2162
379	ZNF473	TF	86.67	86.34	92.54	93	2252
380	MXD4	TF	86.63	84.43	91.34	88.33	18180
381	ZNF707	TF	86.61	86.66	93.38	93.31	3329
382	CREM	TF	86.61	86.56	92.96	93.26	72466
383	ZNF157	TF	86.6	86.52	89.54	86.21	3778
384	IKZF3	TF	86.59	85.8	91.99	88.04	29535
385	DIDO1	TF	86.58	85.66	92.29	92.48	7186
386	ZSCAN26	TF	86.56	85.08	93.43	94.67	2537
387	MXI1	TF	86.53	86.12	94.05	94.26	52982
388	ZSCAN18	TF	86.51	85.15	92.3	92.92	4130
389	CDC5L	TF	86.47	85.08	93.59	93.67	5151
390	KLF5	TF	86.44	85.35	92.7	90.15	11680
391	ZNF512B	TF	86.43	83.44	93.26	91.76	8552
392	LARP7	TF	86.42	84.12	93.32	92.81	27160
393	ZNF280C	TF	86.42	86.07	92.27	92.66	1292
394	L3MBTL2	TF	86.41	86.23	91.05	89.82	52245
395	MCM2	TF	86.41	85.41	93.45	94.29	4549
396	ZNF404	TF	86.4	85.45	91.88	93.7	2249
397	E2F7	TF	86.4	85.34	91.15	91.4	2985
398	MTA1	TF	86.34	84.24	93.57	92.13	22370
399	ZNF324	TF	86.32	84.57	93.81	93.44	14713
400	GTF2F1	TF	86.32	83.54	92.14	90.16	39350
401	RAD21	TF	86.3	97.92	99.11	98.99	188052
402	NR2C1	TF	86.27	81.88	90.51	85.79	31898
403	RBAK	TF	86.25	85.74	92.56	93.16	3642
404	TCF7	TF	86.23	85.39	92.08	90.33	30462
405	ZNF776	TF	86.23	85.19	92.22	92.04	2838
406	ARHGAP35	TF	86.18	85.43	93.57	93.39	4817
407	STAT1	TF	86.15	83.28	92.57	90.18	11457
408	ZNF621	TF	86.14	85.57	92.51	92.93	1976
409	YBX3	TF	86.12	84.54	90.9	90.72	2599
410	ZNF610	TF	86.07	84.35	91.36	89.32	13333
411	OVOL3	TF	86.05	85.14	90.46	88.66	9089
412	GLI2	TF	86.05	86.28	91.17	92.26	5650
413	KLF6	TF	86.05	84.14	91.14	87.94	15409
414	ASH1L	TF	85.96	84.17	92.97	93.93	7269
415	NR3C1	TF	85.91	85.89	93.29	93.1	62779
416	KLF16	TF	85.91	85.24	90.83	90.08	48641
417	ZNF114	TF	85.91	82.83	91.36	91.57	1444
418	PRDM10	TF	85.9	86.39	91.62	88.42	68962
419	ZSCAN29	TF	85.87	82.16	90.3	85.84	21597
420	IRF1	TF	85.84	80.68	89.75	87.82	32357
421	ZSCAN9	TF	85.83	84.87	91.14	89.95	17526
422	ZFP3	TF	85.82	84.76	93.06	93.73	4550
423	TAF7	TF	85.79	81.76	93.28	92.37	21002
424	MNT	TF	85.79	85.08	92.76	93.16	83589
425	ZFP37	TF	85.78	83.76	89.27	86.32	16553
426	MZF1	TF	85.78	85.16	91.67	89.93	17643
427	TOE1	TF	85.74	82.45	89.5	89.69	29556
428	PHF21A	TF	85.74	85.18	88.24	82.19	8878
429	BACH1	TF	85.62	83.64	90.78	88.15	41151
430	ZNF7	TF	85.61	84.92	92.67	92.68	8038
431	ZNF211	TF	85.59	84.6	91.95	92.44	1919
432	ZSCAN23	TF	85.58	84.31	92.3	91.5	8505
433	FOXM1	TF	85.57	83.72	90.82	89.44	20757
434	SUPT5H	TF	85.56	81.99	93.26	92.1	22469
435	BCL3	TF	85.55	83.8	93.27	92.67	43282
436	TFDP1	TF	85.52	80.8	89.14	84.38	30292
437	TAF9B	TF	85.46	83.58	87.02	79.88	13069
438	ZNF792	TF	85.46	83.82	92.95	91.81	24699
439	SIN3A	TF	85.43	85.07	93.29	93.11	65597
440	JUND	TF	85.43	85.33	93.1	93.42	166033
441	H3K9me1	HISTONE	85.43	87.45	93.75	91.95	196657
442	BCL11A	TF	85.41	84.36	92.15	91.13	33663
443	POLR2G	TF	85.39	84.83	92.98	93.64	59528
444	H3K23me2	HISTONE	85.39	85.45	93.76	93.34	77099
445	NR2C2	TF	85.39	80.24	89.73	86.9	29811
446	ZNF571	TF	85.34	84.53	92.7	93.55	1488
447	ZNF311	TF	85.34	84.08	92.44	93.57	2206
448	EP400	TF	85.29	82.21	89.96	88.24	25324
449	ZFP1	TF	85.26	83.98	91.92	90.8	12129
450	REST	TF	85.25	84.97	90.84	91.49	119743
451	RCOR2	TF	85.25	84.38	90.5	88.89	19532
452	SP1	TF	85.24	84.86	91.19	91.14	120925
453	MCM3	TF	85.24	84.32	93	93.26	2561
454	ZNF169	TF	85.23	84.36	91.23	90.6	2873
455	PHF5A	TF	85.23	82.4	90.52	88.55	9570
456	TSHZ1	TF	85.17	84.45	92.39	91.76	11804
457	MTA2	TF	85.15	84.91	90.5	89.57	59001
458	GFI1B	TF	85.11	84.57	91.26	90.52	10694
459	ZNF558	TF	85.1	84.16	91.1	91.2	13849
460	ZNF19	TF	85.06	84.17	91.34	93.34	1998
461	SMAD5	TF	85.03	79.12	92.23	90.37	22402
462	SNRNP70	TF	85.02	82.87	89.28	89.69	871

Model Details

Property	Value
Base model	DNABERT (6-mer, k=6)
Architecture	BERT-base (~340M parameters)
Task	Binary classification (binding/no-binding)
Input	301 bp DNA sequence (6-mer tokenized)
Training data	ENCODE ChIP-seq
Species	Human (hg38)
License	CC-BY-NC-4.0

Citation

@article{deepvregulome2025,
  title={DeepVRegulome: DNABERT-based deep-learning framework for predicting
         the functional impact of short genomic variants on the human regulome},
  author={Dutta, Pratik and Sarkar, Shayan and Sathian, Rekha and Tasnim,
          Taharina and Sibi, Sahanya and Sahanya, Samantha and Ghosal,
          Tirthankar and Ay, Ferhat and Zhong, Zhihan and Han, Jiayu
          and Davuluri, Ramana V.},
  journal={arXiv preprint arXiv:2511.09026},
  year={2025},
  url={https://arxiv.org/abs/2511.09026}
}