Variant report

Variant	esv3356899
Chromosome Location	chr4:653228-653340
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	ARID3A	chr4:652831-653271	HepG2	liver:	n/a	n/a
2	BHLHE40	chr4:652747-653269	HepG2	liver:	n/a	n/a
3	CTCF	chr4:653300-653450	HepG2	liver:	n/a	n/a
4	CTCF	chr4:653260-653410	HepG2	liver:	n/a	n/a
5	EP300	chr4:652811-653280	HepG2	liver:	n/a	n/a
6	EP300	chr4:652790-653234	HepG2	liver:	n/a	n/a
7	FOXA1	chr4:652659-653376	HepG2	liver:	n/a	n/a
8	FOXA1	chr4:652671-653343	HepG2	liver:	n/a	n/a
9	FOXA1	chr4:652691-653262	HepG2	liver:	n/a	n/a
10	FOXA1	chr4:652740-653259	HepG2	liver:	n/a	n/a
11	FOXA2	chr4:652853-653231	HepG2	liver:	n/a	n/a
12	FOXA2	chr4:652511-653380	HepG2	liver:	n/a	n/a
13	HNF4A	chr4:652893-653264	HepG2	liver:	n/a	n/a
14	MAX	chr4:652437-653567	HepG2	liver:	n/a	chr4:653422-653432 chr4:653369-653379 chr4:652843-652852 chr4:653434-653444 chr4:653412-653422
15	MAX	chr4:652724-653576	HepG2	liver:	n/a	chr4:653422-653432 chr4:653369-653379 chr4:652843-652852 chr4:653434-653444 chr4:653412-653422
16	MAX	chr4:653136-653620	H1-hESC	embryonic stem cell:	n/a	chr4:653422-653432 chr4:653369-653379 chr4:653434-653444 chr4:653412-653422
17	MAX	chr4:653155-653698	HUVEC	blood vessel:	n/a	chr4:653422-653432 chr4:653369-653379 chr4:653434-653444 chr4:653412-653422
18	MAX	chr4:653180-653624	NB4	blood:	n/a	chr4:653422-653432 chr4:653369-653379 chr4:653434-653444 chr4:653412-653422
19	MAX	chr4:653155-653512	A549	lung:	n/a	chr4:653422-653432 chr4:653369-653379 chr4:653434-653444 chr4:653412-653422
20	MXI1	chr4:652723-653579	HepG2	liver:	n/a	n/a
21	MYBL2	chr4:652653-653326	HepG2	liver:	n/a	n/a
22	NFIC	chr4:652755-653269	HepG2	liver:	n/a	n/a
23	NR2C2	chr4:653286-653799	GM12878	blood:	n/a	n/a
24	POLR2A	chr4:653142-653544	GM12878	blood:	n/a	n/a
25	POLR2A	chr4:653308-653419	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr4:653127-653856	Raji	blood:	n/a	n/a
27	POLR2A	chr4:653238-653511	GM12878	blood:	n/a	n/a
28	POLR2A	chr4:653247-653414	Gliobla	brain:	n/a	n/a
29	POLR2A	chr4:653134-653501	H1-hESC	embryonic stem cell:	n/a	n/a
30	RCOR1	chr4:652802-653424	HepG2	liver:	n/a	n/a
31	REST	chr4:652772-653251	HepG2	liver:	n/a	n/a
32	SP1	chr4:653170-653297	HepG2	liver:	n/a	n/a
33	SP1	chr4:652774-653334	HepG2	liver:	n/a	n/a
34	SUZ12	chr4:653037-653961	H1-hESC	embryonic stem cell:	n/a	n/a
35	TCF12	chr4:652868-653420	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:647827..650169-chr4:651801..653823,2	K562	blood:
2	chr4:641525..644066-chr4:652058..654958,2	K562	blood:

Variant related genes	Relation type
ENSG00000242686	TF binding region
PDE6B	TF binding region
ENSG00000242686	chromatin interactions

Extended variants
information (count: 13 )
Associated
traits (count: 66 )

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs115085351	chr4:653255-653256	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
2	rs368904134	chr4:653271-653272	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs554304759	chr4:653275-653276	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
4	rs540220222	chr4:653277-653278	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
5	rs139289207	chr4:653290-653291	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
6	rs546241111	chr4:653291-653292	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
7	rs374246446	chr4:653293-653294	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
8	rs561557135	chr4:653308-653309	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
9	rs540135807	chr4:653315-653316	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
10	rs565212603	chr4:653322-653323	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
11	rs60316402	chr4:653327-653328	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
12	rs139464207	chr4:653330-653331	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
13	rs373526774	chr4:653331-653332	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:66)

Disease	PMID	Source
Myelofibrosis	22110671	CNVD
Wolf-Hirschhorn syndrome	21549014	CNVD
Breast cancer	21806811	CNVD
Wolf-Hirschhorn syndrome	22283845	CNVD
Wolf-Hirschhorn syndrome	16773131	CNVD
Mental retardation	16773131	CNVD
Wolf-Hirschhorn syndrome	22470819	CNVD
Wolf-Hirschhorn syndrome	18541967	CNVD
sporadic birth defects	19047251	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Retinitis pigmentosa	18421352	CNVD
Wolf-Hirschhorn syndrome	19259404	CNVD
Bladder cancer	19242612	CNVD
Breast cancer	19242612	CNVD
Congenital anomalies of the kidney and urinary tract	19242612	CNVD
abnormal development	18461090	CNVD
Olfactory neuroblastoma	18408657	CNVD
Wilms tumour	21544195	CNVD
Melanoma	20688739	CNVD
Colorectal cancer	16272173	CNVD
Non-syndromic sensorineural hearing loss	20606397	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	17603634	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Colorectal cancer	19359472	CNVD
Neuroblastoma	17533364	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Cancer	21637783	CNVD
Melanoma	21693616	CNVD
Squamous cell cancer	21044232	CNVD
Colorectal cancer	20709793	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Non-small cell lung cancer	21044232	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	17387387	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Cervical cancer	21062161	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Glioblastoma multiforme	21080181	CNVD
Chordoma	21602918	CNVD
HIV/AIDS	22032296	CNVD
Neuroblastoma	18923191	CNVD
small cell lung cancer	20016488	CNVD
Breast cancer	17142309	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Developmental delay	21147756	CNVD
Urothelial carcinoma	21177765	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Lung cancer	18438408	CNVD
Prostate cancer	18632612	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
Pancreatic cancer	17952125	CNVD
Type 2 diabetes	21754918	CNVD
Breast cancer	22522925	CNVD
Breast cancer	21509527	CNVD
Glioma	20126413	CNVD

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:631400-657000	Weak transcription	Right Atrium	heart
2	chr4:641800-657000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr4:642400-654600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr4:642800-657000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:643000-657000	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr4:645800-656800	Weak transcription	Gastric	stomach
7	chr4:648400-657000	Weak transcription	Right Ventricle	heart
8	chr4:648800-653400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr4:649800-655600	Weak transcription	Thymus	Thymus
10	chr4:650000-654000	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr4:650000-654200	Enhancers	HepG2	liver
12	chr4:650800-656000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr4:651000-653600	Weak transcription	Fetal Brain Male	brain
14	chr4:651200-654400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr4:651400-653400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr4:651400-656400	Weak transcription	Pancreas	Pancrea
17	chr4:651600-657000	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr4:651600-657200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr4:651800-656800	Weak transcription	Primary B cells from cord blood	blood
20	chr4:652000-653600	Weak transcription	Fetal Stomach	stomach
21	chr4:652000-656800	Weak transcription	Fetal Lung	lung
22	chr4:652200-654000	Genic enhancers	Spleen	Spleen
23	chr4:652400-655200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr4:652400-656800	Weak transcription	Primary hematopoietic stem cells	blood
25	chr4:652600-654000	Strong transcription	Brain Anterior Caudate	brain
26	chr4:652600-656800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr4:652600-656800	Weak transcription	Fetal Thymus	thymus
28	chr4:652800-653600	Strong transcription	Primary T cells from cord blood	blood
29	chr4:652800-653600	Strong transcription	Brain Angular Gyrus	brain
30	chr4:652800-653600	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
31	chr4:652800-653800	Strong transcription	Brain Hippocampus Middle	brain
32	chr4:652800-654000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
33	chr4:652800-654400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr4:652800-654400	Strong transcription	Brain Substantia Nigra	brain
35	chr4:652800-656000	Strong transcription	Brain Germinal Matrix	brain
36	chr4:653000-654600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr4:653000-655600	Weak transcription	Lung	lung
38	chr4:653000-656800	Weak transcription	Fetal Heart	heart
39	chr4:653000-657000	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr4:653200-653400	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
41	chr4:653200-653400	Active TSS	Breast Myoepithelial Primary Cells	Breast
42	chr4:653200-654000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr4:653200-654600	Strong transcription	Brain Inferior Temporal Lobe	brain
44	chr4:653200-654600	Strong transcription	Fetal Intestine Small	intestine
45	chr4:653200-655600	Strong transcription	Dnd41	blood
46	chr4:653200-655800	Strong transcription	Cortex derived primary cultured neurospheres	brain
47	chr4:653200-656200	Strong transcription	Fetal Brain Female	brain
48	chr4:653200-656400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr4:653200-656800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr4:653200-657000	Weak transcription	Fetal Kidney	kidney

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