Variant report

Variant	esv15254
Chromosome Location	chr4:79697089-79697707
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ATF3	chr4:79696936-79697176	H1-hESC	embryonic stem cell:	n/a	chr4:79697136-79697145 chr4:79696955-79696975
2	ATF3	chr4:79696926-79697242	HepG2	liver:	n/a	chr4:79697136-79697145 chr4:79696955-79696975
3	ATF3	chr4:79696969-79697245	GM12878	blood:	n/a	chr4:79697136-79697145
4	ATF3	chr4:79696931-79697257	K562	blood:	n/a	chr4:79697136-79697145 chr4:79696955-79696975
5	ATF3	chr4:79696914-79697196	H1-hESC	embryonic stem cell:	n/a	chr4:79697136-79697145 chr4:79696955-79696975
6	ATF3	chr4:79696845-79697321	GM12878	blood:	n/a	chr4:79697136-79697145 chr4:79696955-79696975
7	ATF3	chr4:79696803-79697243	HepG2	liver:	n/a	chr4:79697136-79697145 chr4:79696955-79696975
8	BACH1	chr4:79696692-79697359	H1-hESC	embryonic stem cell:	n/a	n/a
9	BCLAF1	chr4:79697391-79697750	GM12878	blood:	n/a	chr4:79697628-79697641 chr4:79697627-79697640
10	BCLAF1	chr4:79696557-79697238	GM12878	blood:	n/a	chr4:79697134-79697147 chr4:79697127-79697136 chr4:79697147-79697160
11	BCLAF1	chr4:79696468-79697447	GM12878	blood:	n/a	chr4:79697323-79697336 chr4:79697134-79697147 chr4:79697127-79697136 chr4:79697147-79697160
12	BCLAF1	chr4:79697110-79697706	K562	blood:	n/a	chr4:79697323-79697336 chr4:79697134-79697147 chr4:79697628-79697641 chr4:79697127-79697136 chr4:79697627-79697640 chr4:79697147-79697160
13	BHLHE40	chr4:79696445-79697724	K562	blood:	n/a	chr4:79697495-79697511 chr4:79697622-79697638 chr4:79697630-79697646
14	BHLHE40	chr4:79696276-79697722	GM12878	blood:	n/a	chr4:79697495-79697511 chr4:79697622-79697638 chr4:79697630-79697646
15	BHLHE40	chr4:79696606-79697696	HepG2	liver:	n/a	chr4:79697495-79697511 chr4:79697622-79697638 chr4:79697630-79697646
16	BRCA1	chr4:79697140-79697152	HepG2	liver:	n/a	n/a
17	CBX3	chr4:79696528-79697234	K562	blood:	n/a	n/a
18	CCNT2	chr4:79696809-79698067	K562	blood:	n/a	chr4:79697915-79697924 chr4:79697068-79697077
19	CEBPB	chr4:79696128-79697224	Hela-S3	cervix:	n/a	n/a
20	CEBPD	chr4:79696880-79697788	K562	blood:	n/a	n/a
21	CEBPD	chr4:79697208-79697436	HepG2	liver:	n/a	n/a
22	CEBPD	chr4:79696855-79697699	HepG2	liver:	n/a	n/a
23	CHD1	chr4:79695833-79697696	GM12878	blood:	n/a	n/a
24	CHD2	chr4:79696642-79697191	H1-hESC	embryonic stem cell:	n/a	n/a
25	CHD2	chr4:79696255-79697689	Hela-S3	cervix:	n/a	n/a
26	CHD2	chr4:79696686-79697418	HepG2	liver:	n/a	n/a
27	CHD2	chr4:79696623-79697521	GM12878	blood:	n/a	n/a
28	CHD2	chr4:79696510-79697280	K562	blood:	n/a	n/a
29	CREB1	chr4:79696500-79697364	H1-hESC	embryonic stem cell:	n/a	n/a
30	CREB1	chr4:79696880-79697233	ECC-1	luminal epithelium:	n/a	n/a
31	CREB1	chr4:79696466-79697748	HepG2	liver:	n/a	n/a
32	CREB1	chr4:79696701-79697405	H1-hESC	embryonic stem cell:	n/a	n/a
33	CREB1	chr4:79696958-79697235	A549	lung:	n/a	n/a
34	CREB1	chr4:79696610-79697509	A549	lung:	n/a	n/a
35	CREB1	chr4:79696550-79697705	GM12878	blood:	n/a	n/a
36	CTBP2	chr4:79696593-79698523	H1-hESC	embryonic stem cell:	n/a	n/a
37	CTCF	chr4:79697461-79697664	HepG2	liver:	n/a	chr4:79697609-79697627 chr4:79697610-79697626
38	CTCF	chr4:79697460-79697610	GM12873	blood:	n/a	n/a
39	CTCF	chr4:79697660-79697665	MCF-7	breast:	n/a	n/a
40	CTCF	chr4:79697520-79697670	GM12870	blood:	n/a	chr4:79697609-79697627 chr4:79697610-79697626
41	CTCF	chr4:79697520-79697670	AG04449	skin:	n/a	chr4:79697609-79697627 chr4:79697610-79697626
42	CTCF	chr4:79697504-79697666	LNCaP	prostate:	n/a	chr4:79697609-79697627 chr4:79697610-79697626
43	CTCF	chr4:79697500-79697650	SAEC	small airway:	n/a	chr4:79697609-79697627 chr4:79697610-79697626
44	CTCF	chr4:79697456-79697723	H1-hESC	embryonic stem cell:	n/a	chr4:79697609-79697627 chr4:79697610-79697626
45	CTCF	chr4:79697541-79697624	GM13977	blood:	n/a	n/a
46	CTCF	chr4:79697540-79697690	GM12872	blood:	n/a	chr4:79697609-79697627 chr4:79697610-79697626
47	CTCF	chr4:79697500-79697650	WERI-Rb-1	eye:	n/a	chr4:79697609-79697627 chr4:79697610-79697626
48	CTCF	chr4:79697540-79697690	GM12868	blood:	n/a	chr4:79697609-79697627 chr4:79697610-79697626
49	CTCF	chr4:79697480-79697630	GM12869	blood:	n/a	chr4:79697609-79697627 chr4:79697610-79697626
50	CTCF	chr4:79697400-79697550	GM12867	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:79697329-79697379	GM06990	blood:	n/a
2	chr4:79697329-79697379	GM06990	blood:	n/a
3	chr4:79697329-79697379	ovcar-3	ovarian:	n/a
4	chr4:79697583-79697633	Hepatocyte	liver:	n/a
5	chr4:79697583-79697633	Jurkat	blood:	n/a
6	chr4:79697329-79697379	GM12892	blood:	n/a
7	chr4:79697329-79697379	HCF	heart:	n/a
8	chr4:79697329-79697379	NB4	blood:	n/a
9	chr4:79697583-79697633	PANC-1	pancreas:	n/a
10	chr4:79697329-79697379	RPTEC	kidney:	n/a
11	chr4:79697583-79697633	PFSK-1	brain:	n/a
12	chr4:79697329-79697379	SKMC	muscle:	n/a
13	chr4:79697583-79697633	HCT-116	colon:	n/a
14	chr4:79697583-79697633	MCF-7	breast:	n/a
15	chr4:79697329-79697379	Jurkat	blood:	n/a
16	chr4:79697583-79697633	PrEC	prostate:	n/a
17	chr4:79697583-79697633	GM12878	blood:	n/a
18	chr4:79697583-79697633	HPAEpiC	pulmonary alveolar:	n/a
19	chr4:79697583-79697633	ProgFib	skin:	n/a
20	chr4:79697583-79697633	BJ	skin:	n/a
21	chr4:79697583-79697633	BE2_C	brain:	n/a
22	chr4:79697329-79697379	HCM	heart:	n/a
23	chr4:79697329-79697379	HEEpiC	esophagus:	n/a
24	chr4:79697329-79697379	HCT-116	colon:	n/a
25	chr4:79697329-79697379	CMK	blood:	n/a
26	chr4:79697583-79697633	HCM	heart:	n/a
27	chr4:79697583-79697633	NB4	blood:	n/a
28	chr4:79697583-79697633	SK-N-SH_RA	brain:	n/a
29	chr4:79697329-79697379	GM12891	blood:	n/a
30	chr4:79697329-79697379	PFSK-1	brain:	n/a
31	chr4:79697583-79697633	SK-N-SH	brain:	n/a
32	chr4:79697329-79697379	SK-N-MC	brain:	n/a
33	chr4:79697329-79697379	AG04450	lung:	fetal
34	chr4:79697329-79697379	SK-N-SH_RA	brain:	n/a
35	chr4:79697583-79697633	HUVEC	blood vessel:	n/a
36	chr4:79697583-79697633	MCF10A-Er-Src	breast:	n/a
37	chr4:79697329-79697379	Hepatocyte	liver:	n/a
38	chr4:79697583-79697633	ECC-1	luminal epithelium:	n/a
39	chr4:79697329-79697379	HAEpiC	amniotic membrane:	n/a
40	chr4:79697583-79697633	AoSMC	blood vessel:	n/a
41	chr4:79697583-79697633	RPTEC	kidney:	n/a
42	chr4:79697329-79697379	AG09319	gingival:	n/a
43	chr4:79697329-79697379	BJ	skin:	n/a
44	chr4:79697329-79697379	ProgFib	skin:	n/a
45	chr4:79697329-79697379	AG04449	skin:	fetal
46	chr4:79697583-79697633	LNCaP	prostate:	n/a
47	chr4:79697583-79697633	NHBE	bronchial:	n/a
48	chr4:79697329-79697379	AoSMC	blood vessel:	n/a
49	chr4:79697329-79697379	NH-A	brain:	n/a
50	chr4:79697329-79697379	GM12878	blood:	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:79686100..79693924-chr4:79694940..79698947,11	MCF-7	breast:
2	chr4:79696772..79697553-chr6:43737917..43738589,2	Hela-S3	cervix:
3	chr4:79568346..79573757-chr4:79695931..79699478,7	MCF-7	breast:
4	chr4:79564080..79567985-chr4:79696414..79698633,7	MCF-7	breast:
5	chr12:6309195..6310003-chr4:79696831..79697536,2	Hela-S3	cervix:
6	chr4:79570295..79572982-chr4:79695014..79699413,6	MCF-7	breast:
7	chr4:79562196..79569044-chr4:79695847..79699797,11	MCF-7	breast:
8	chr4:79522193..79524527-chr4:79697309..79699707,2	MCF-7	breast:
9	chr4:79697362..79698154-chrX:118601587..118602475,2	HCT-116	colon:
10	chr4:79697257..79699576-chr4:79770892..79773352,2	MCF-7	breast:
11	chr4:79591975..79594296-chr4:79697576..79699186,2	K562	blood:
12	chr4:79696515..79698358-chr4:79778442..79780983,2	K562	blood:
13	chr4:79522884..79525832-chr4:79695803..79698616,2	K562	blood:
14	chr4:79565693..79569294-chr4:79696000..79698136,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PAQR3-1	chr4:79694808-79697127	ENSG00000260278.1

Variant related genes	Relation type
ENSG00000260278	TF binding region
BMP2K	TF binding region
ENSG00000260278	CpG island
BMP2K	CpG island
ENSG00000112715	chromatin interactions
ENSG00000224281	chromatin interactions
ENSG00000251019	chromatin interactions
ENSG00000010278	chromatin interactions
ENSG00000251442	chromatin interactions
ENSG00000239793	chromatin interactions
ENSG00000138772	chromatin interactions
ENSG00000272114	chromatin interactions
ENSG00000138756	chromatin interactions
ENSG00000005022	chromatin interactions

Extended variants
information (count: 15 )
Associated
traits (count: 77 )

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs553247698	chr4:79697142-79697143	Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS	TF binding region Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
2	rs375459717	chr4:79697151-79697152	Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS	TF binding region Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
3	rs553002533	chr4:79697175-79697176	Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS	TF binding region Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
4	rs111888491	chr4:79697190-79697191	Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS	TF binding region Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
5	rs71216234	chr4:79697210-79697211	Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
6	rs573023688	chr4:79697270-79697271	Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
7	rs147417383	chr4:79697281-79697282	Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
8	rs558513234	chr4:79697412-79697413	Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region Chromatin interactive region	12 gene(s)	Overlapped CNVs	n/a
9	rs575578180	chr4:79697450-79697451	Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region Chromatin interactive region	12 gene(s)	Overlapped CNVs	n/a
10	rs139143500	chr4:79697540-79697541	Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
11	rs563478630	chr4:79697547-79697548	Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
12	rs548621984	chr4:79697641-79697642	Active TSS Weak transcription Bivalent/Poised TSS	TF binding region Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
13	rs542863685	chr4:79697673-79697674	Active TSS Weak transcription Bivalent/Poised TSS	TF binding region Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
14	rs559454547	chr4:79697688-79697689	Active TSS Weak transcription Bivalent/Poised TSS	TF binding region Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
15	rs528176559	chr4:79697696-79697697	Active TSS Weak transcription Bivalent/Poised TSS	TF binding region Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:77)

Disease	PMID	Source
Acute lymphoblastic leukemia	22237106	CNVD
Glioblastoma multiforme	21080181	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Chordoma	21602918	CNVD
HIV/AIDS	22032296	CNVD
Medulloblastoma	21979893	CNVD
Neuroblastoma	18923191	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Breast cancer	21858162	CNVD
Small bowel adenocarcinoma	21586687	CNVD
Gastric cancer	21586687	CNVD
lymphocytic leukemia	21291569	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Melanoma	18172304	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Breast cancer	17603634	CNVD
Glioblastoma multiforme	21922591	CNVD
Parkinson disease	21956041	CNVD
Mental retardation	20522426	CNVD
delayed speech	20522426	CNVD
growth disorder	20522426	CNVD
Hepatocellular carcinoma	16750200	CNVD
Myxofibrosarcoma	16751306	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Parkinson disease	18923514	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Cancer	21183584	CNVD
Breast cancer	16272173	CNVD
Colorectal cancer	19359472	CNVD
Malignant mesothelioma	18160781	CNVD
Medulloblastoma	18056178	CNVD
Multiple myeloma	17077331	CNVD
Pleural malignant mesothelioma	18160781	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Oral squamous cell carcinoma	17134496	CNVD
4q-syndrome	17576883	CNVD
Cancer	21637783	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Colorectal cancer	20709793	CNVD
Muscular dystrophy	21149563	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	17387387	CNVD
Hepatocellular carcinoma	22174799	CNVD
Liposarcoma	21253554	CNVD
Oligodendroglial tumors	17285580	CNVD
Cervical cancer	21062161	CNVD
Metanephric adenoma	20802469	CNVD
Breast cancer	16608533	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Lung cancer	19208797	CNVD
Wilms tumour	21544195	CNVD
Breast cancer	21785460	CNVD
Basal cell lymphoma	17170743	CNVD
Follicular lymphoma	17170743	CNVD
Chronic lymphocytic leukemia	20421269	CNVD
Myelodysplastic syndrome	21251322	CNVD
Multiple myeloma	17550852	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Chronic lymphocytic leukemia	18922857	CNVD
Cancer	22429812	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Autism	18414403	CNVD
Chronic lymphocytic leukemia	21670202	CNVD
primary effusion lymphomas	17116491	CNVD
Gastric cancer	16891809	CNVD
Prostate cancer	16573809	CNVD
Myelofibrosis	22110671	CNVD
Neuroblastoma	21899760	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:132 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79695800-79698200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr4:79695800-79698800	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr4:79696000-79697200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr4:79696000-79698000	Active TSS	Stomach Smooth Muscle	stomach
5	chr4:79696000-79698400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr4:79696000-79698800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr4:79696000-79699000	Active TSS	Hela-S3	cervix
8	chr4:79696000-79699600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr4:79696000-79699800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr4:79696200-79697800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr4:79696200-79698000	Active TSS	Skeletal Muscle Female	skeletal muscle
12	chr4:79696200-79698200	Active TSS	Brain Anterior Caudate	brain
13	chr4:79696200-79698200	Active TSS	Brain Inferior Temporal Lobe	brain
14	chr4:79696200-79698200	Active TSS	Colonic Mucosa	Colon
15	chr4:79696200-79698200	Active TSS	Duodenum Mucosa	Duodenum
16	chr4:79696200-79698400	Active TSS	Primary T helper naive cells from peripheral blood	blood
17	chr4:79696200-79698400	Active TSS	Pancreatic Islets	Pancreatic Islet
18	chr4:79696200-79698600	Active TSS	Ovary	ovary
19	chr4:79696200-79698800	Active TSS	H9 Cell Line	embryonic stem cell
20	chr4:79696200-79698800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr4:79696200-79698800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr4:79696200-79698800	Active TSS	Aorta	Aorta
23	chr4:79696200-79698800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
24	chr4:79696200-79698800	Active TSS	A549	lung
25	chr4:79696200-79699000	Active TSS	iPS-15b Cell Line	embryonic stem cell
26	chr4:79696200-79699200	Active TSS	ES-I3 Cell Line	embryonic stem cell
27	chr4:79696200-79699200	Active TSS	H1 Cell Line	embryonic stem cell
28	chr4:79696200-79699200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr4:79696200-79699200	Active TSS	Fetal Kidney	kidney
30	chr4:79696200-79699200	Active TSS	Fetal Muscle Trunk	muscle
31	chr4:79696200-79699200	Active TSS	Fetal Stomach	stomach
32	chr4:79696200-79699200	Active TSS	Psoas Muscle	Psoas
33	chr4:79696200-79699600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr4:79696200-79699600	Active TSS	HUES6 Cell Line	embryonic stem cell
35	chr4:79696200-79699600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr4:79696200-79699800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr4:79696200-79699800	Active TSS	Duodenum Smooth Muscle	Duodenum
38	chr4:79696200-79699800	Active TSS	Thymus	Thymus
39	chr4:79696200-79699800	Active TSS	NHDF-Ad	bronchial
40	chr4:79696200-79700200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr4:79696200-79700800	Active TSS	Rectal Smooth Muscle	rectum
42	chr4:79696400-79697200	Active TSS	Primary T killer memory cells from peripheral blood	blood
43	chr4:79696400-79698200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr4:79696400-79698200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
45	chr4:79696400-79698200	Active TSS	Brain Substantia Nigra	brain
46	chr4:79696400-79698400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr4:79696400-79698400	Active TSS	Colon Smooth Muscle	Colon
48	chr4:79696400-79698400	Active TSS	Fetal Lung	lung
49	chr4:79696400-79698600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr4:79696400-79698600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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