Variant report

Variant	esv3500540
Chromosome Location	chr4:661848-664051
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:133)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:133 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BCL11A	chr4:662434-663124	GM12878	blood:	n/a	n/a
2	BCL11A	chr4:663228-663616	GM12878	blood:	n/a	n/a
3	CHD2	chr4:663597-663787	K562	blood:	n/a	n/a
4	ELF1	chr4:663647-664020	GM12878	blood:	n/a	n/a
5	EP300	chr4:662981-663252	SK-N-SH_RA	brain:	n/a	n/a
6	FOSL2	chr4:662988-663635	HepG2	liver:	n/a	n/a
7	FOSL2	chr4:662221-662617	HepG2	liver:	n/a	n/a
8	FOXA1	chr4:663547-663692	T-47D	breast:	n/a	n/a
9	HEY1	chr4:662185-663145	K562	blood:	n/a	n/a
10	HEY1	chr4:663154-663347	HepG2	liver:	n/a	n/a
11	IRF4	chr4:662136-663053	GM12878	blood:	n/a	n/a
12	IRF4	chr4:663125-663639	GM12878	blood:	n/a	n/a
13	JUND	chr4:663024-663552	HepG2	liver:	n/a	n/a
14	JUND	chr4:663236-663544	HepG2	liver:	n/a	n/a
15	NFATC1	chr4:663551-664030	GM12878	blood:	n/a	n/a
16	NFATC1	chr4:663535-663963	GM12878	blood:	n/a	n/a
17	PAX5	chr4:663272-663583	GM12878	blood:	n/a	n/a
18	PAX5	chr4:663262-663576	GM12878	blood:	n/a	n/a
19	PAX5	chr4:662432-662766	GM12878	blood:	n/a	n/a
20	PBX3	chr4:662264-663545	GM12878	blood:	n/a	n/a
21	PBX3	chr4:662279-663545	GM12878	blood:	n/a	n/a
22	POLR2A	chr4:662530-662658	A549	lung:	n/a	n/a
23	POLR2A	chr4:663493-664038	ECC-1	luminal epithelium:	n/a	n/a
24	POLR2A	chr4:662048-662335	ECC-1	luminal epithelium:	n/a	n/a
25	POLR2A	chr4:662827-662984	A549	lung:	n/a	n/a
26	POLR2A	chr4:663968-665297	PFSK-1	brain:	n/a	n/a
27	POLR2A	chr4:663170-663859	SK-N-SH	brain:	n/a	n/a
28	POLR2A	chr4:663495-664064	K562	blood:	n/a	n/a
29	POLR2A	chr4:663593-663992	GM12878	blood:	n/a	n/a
30	POLR2A	chr4:663579-663983	Hela-S3	cervix:	n/a	n/a
31	POLR2A	chr4:661846-662348	Raji	blood:	n/a	n/a
32	POLR2A	chr4:662085-663984	GM12892	blood:	n/a	n/a
33	POLR2A	chr4:660331-662344	K562	blood:	n/a	n/a
34	POLR2A	chr4:662051-663649	GM12891	blood:	n/a	n/a
35	POLR2A	chr4:663314-663548	A549	lung:	n/a	n/a
36	POLR2A	chr4:662127-663941	H1-hESC	embryonic stem cell:	n/a	n/a
37	POLR2A	chr4:663253-663554	A549	lung:	n/a	n/a
38	POLR2A	chr4:663303-663771	PANC-1	pancreas:	n/a	n/a
39	POLR2A	chr4:663539-663922	K562	blood:	n/a	n/a
40	POLR2A	chr4:663113-666359	SK-N-MC	brain:	n/a	n/a
41	POLR2A	chr4:662911-664023	H1-hESC	embryonic stem cell:	n/a	n/a
42	POLR2A	chr4:662960-663996	MCF-7	breast:	n/a	n/a
43	POLR2A	chr4:662029-663984	GM12891	blood:	n/a	n/a
44	POLR2A	chr4:662047-662072	MCF-7	breast:	n/a	n/a
45	POLR2A	chr4:663260-663264	Gliobla	brain:	n/a	n/a
46	POLR2A	chr4:663072-663264	HepG2	liver:	n/a	n/a
47	POLR2A	chr4:663175-663518	HepG2	liver:	n/a	n/a
48	POLR2A	chr4:661582-662506	K562	blood:	n/a	n/a
49	POLR2A	chr4:662971-663109	GM12878	blood:	n/a	n/a
50	POLR2A	chr4:663500-664113	HL-60	blood:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:606087..607621-chr4:663295..666195,2	MCF-7	breast:
2	chr4:640175..641727-chr4:663332..665885,2	K562	blood:
3	chr4:662349..665374-chr4:675709..679343,3	MCF-7	breast:
4	chr4:494928..497132-chr4:662075..663676,2	K562	blood:
5	chr4:663922..666504-chr4:705768..707927,2	MCF-7	breast:
6	chr4:642255..644273-chr4:662905..665187,2	K562	blood:
7	chr4:658187..662144-chr4:672176..676426,5	MCF-7	breast:
8	chr4:608874..610845-chr4:663421..664979,2	K562	blood:
9	chr4:627338..629172-chr4:662112..664476,2	MCF-7	breast:
10	chr4:624127..625792-chr4:659574..661910,2	K562	blood:
11	chr4:663475..665943-chr8:145718684..145721269,2	MCF-7	breast:

No data

Variant related genes	Relation type
MYL5	TF binding region
ENSG00000215375	chromatin interactions
ENSG00000169026	chromatin interactions

Extended variants
information (count: 171 )
Associated
traits (count: 65 )

Variant overlapped rSNPs/rCNVs (count:171 , 50 per page) page: 1 2 3 4

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs537349562	chr4:661863-661864	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
2	rs28568555	chr4:661931-661932	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
3	rs532553970	chr4:661939-661940	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
4	rs28483373	chr4:661955-661956	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
5	rs535094024	chr4:661958-661959	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
6	rs77751621	chr4:661982-661983	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs577729443	chr4:661994-661995	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs138744450	chr4:661995-661996	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs556739634	chr4:662013-662014	Weak transcription Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs575153597	chr4:662023-662024	Weak transcription Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs542595758	chr4:662129-662130	Weak transcription Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs560935073	chr4:662130-662131	Weak transcription Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs577882305	chr4:662132-662133	Weak transcription Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs559583988	chr4:662133-662134	Weak transcription Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs572779647	chr4:662138-662139	Weak transcription Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs540307880	chr4:662178-662179	Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
17	rs564940314	chr4:662218-662219	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs367836411	chr4:662219-662220	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs372034137	chr4:662261-662262	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs75309160	chr4:662270-662271	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs375126496	chr4:662271-662272	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs561047858	chr4:662276-662277	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs199631919	chr4:662278-662279	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs112092979	chr4:662280-662281	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs79510306	chr4:662285-662286	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs371970015	chr4:662288-662289	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs71602497	chr4:662291-662292	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs71166825	chr4:662294-662295	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs532268594	chr4:662303-662304	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs71602710	chr4:662308-662309	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs74215639	chr4:662321-662322	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs551960154	chr4:662329-662330	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs200584585	chr4:662332-662333	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs185853325	chr4:662349-662350	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs200121628	chr4:662350-662351	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs74208028	chr4:662364-662365	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs531229967	chr4:662387-662388	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
38	rs201862699	chr4:662406-662407	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
39	rs549461403	chr4:662412-662413	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
40	rs201223498	chr4:662424-662425	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
41	rs148452311	chr4:662441-662442	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
42	rs200393450	chr4:662462-662463	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
43	rs201787871	chr4:662499-662500	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
44	rs201561063	chr4:662536-662537	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
45	rs111676642	chr4:662545-662546	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
46	rs200318777	chr4:662628-662629	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
47	rs534673155	chr4:662657-662658	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
48	rs546609131	chr4:662670-662671	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
49	rs571359701	chr4:662671-662672	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
50	rs199741731	chr4:662684-662685	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:65)

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
Breast cancer	21509527	CNVD
Pancreatic cancer	17952125	CNVD
Type 2 diabetes	21754918	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:145 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:658000-664400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr4:658000-667000	Weak transcription	Small Intestine	intestine
3	chr4:658000-667400	Weak transcription	Aorta	Aorta
4	chr4:658200-664400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr4:658200-664400	Weak transcription	Colon Smooth Muscle	Colon
6	chr4:658200-664400	Weak transcription	Duodenum Mucosa	Duodenum
7	chr4:658200-664400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr4:658200-664600	Weak transcription	Pancreas	Pancrea
9	chr4:658200-664600	Weak transcription	HUVEC	blood vessel
10	chr4:658200-664800	Weak transcription	Gastric	stomach
11	chr4:658200-665000	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr4:658200-666800	Weak transcription	Right Atrium	heart
13	chr4:658200-667000	Weak transcription	Stomach Mucosa	stomach
14	chr4:658200-667200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr4:658400-662000	Enhancers	Fetal Muscle Trunk	muscle
16	chr4:658400-663600	Weak transcription	Fetal Stomach	stomach
17	chr4:658400-663800	Weak transcription	Primary T cells from cord blood	blood
18	chr4:658400-663800	Weak transcription	Brain Germinal Matrix	brain
19	chr4:658400-664400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr4:658400-664400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr4:658400-664400	Weak transcription	Liver	Liver
22	chr4:658400-664400	Weak transcription	Left Ventricle	heart
23	chr4:658400-664400	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr4:658400-664400	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr4:658400-664400	Weak transcription	Rectal Smooth Muscle	rectum
26	chr4:658400-664400	Weak transcription	HMEC	breast
27	chr4:658400-664600	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr4:658400-664600	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr4:658400-664600	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr4:658400-664600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr4:658400-664600	Weak transcription	Fetal Brain Female	brain
32	chr4:658400-664600	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr4:658400-664600	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr4:658400-664600	Weak transcription	NH-A	brain
35	chr4:658400-664800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr4:658400-665000	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr4:658400-665000	Weak transcription	Fetal Lung	lung
38	chr4:658400-665200	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr4:658400-665200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr4:658400-665200	Weak transcription	Right Ventricle	heart
41	chr4:658400-665400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr4:658400-665400	Weak transcription	Fetal Kidney	kidney
43	chr4:658400-667000	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr4:658600-664400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr4:658600-667000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr4:658600-667000	Weak transcription	Fetal Brain Male	brain
47	chr4:658800-664200	Weak transcription	Thymus	Thymus
48	chr4:658800-664400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr4:658800-664400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr4:658800-664400	Weak transcription	Fetal Thymus	thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links