Variant report

Variant	esv2328657
Chromosome Location	chr4:3389734-3390188
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:3385272..3387718-chr4:3389014..3391654,3	MCF-7	breast:
2	chr4:3388642..3391528-chr4:3405332..3407484,2	MCF-7	breast:
3	chr4:3388406..3390149-chr4:3442407..3445401,2	MCF-7	breast:
4	chr4:3294234..3297919-chr4:3387466..3390148,3	MCF-7	breast:
5	chr4:3356602..3361196-chr4:3388835..3391854,4	MCF-7	breast:
6	chr4:3388256..3390546-chr4:3393263..3395293,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000109758	chromatin interactions
ENSG00000159788	chromatin interactions

Extended variants
information (count: 29 )
Associated
traits (count: 55 )

Variant overlapped rSNPs/rCNVs (count:29 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs538093684	chr4:3389750-3389751	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
2	rs6847900	chr4:3389755-3389756	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
3	rs371829760	chr4:3389758-3389759	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
4	rs373890808	chr4:3389762-3389763	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
5	rs142584426	chr4:3389767-3389768	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
6	rs147604053	chr4:3389798-3389799	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
7	rs142171902	chr4:3389809-3389810	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
8	rs916188	chr4:3389810-3389811	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
9	rs6828057	chr4:3389811-3389812	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
10	rs146086244	chr4:3389821-3389822	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
11	rs188672443	chr4:3389840-3389841	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs576551946	chr4:3389854-3389855	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
13	rs542443383	chr4:3389896-3389897	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
14	rs9761320	chr4:3389909-3389910	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
15	rs374092485	chr4:3389911-3389912	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
16	rs533233269	chr4:3389923-3389924	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
17	rs555762033	chr4:3389951-3389952	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
18	rs6148279	chr4:3389963-3389964	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
19	rs138913052	chr4:3389967-3389968	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
20	rs541343424	chr4:3389985-3389986	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
21	rs564100388	chr4:3390079-3390080	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
22	rs533159392	chr4:3390102-3390103	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
23	rs555802005	chr4:3390117-3390118	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
24	rs78101638	chr4:3390120-3390121	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
25	rs563849051	chr4:3390137-3390138	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
26	rs2269496	chr4:3390146-3390147	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
27	rs140408637	chr4:3390158-3390159	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
28	rs150192728	chr4:3390170-3390171	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs527538084	chr4:3390175-3390176	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:55)

Disease	PMID	Source
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
T-cell prolymphocytic leukemia	19278963	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
Breast cancer	21785460	CNVD
Myelofibrosis	22110671	CNVD
Schizophrenia	21399695	CNVD
Pancreatic ductal adenocarcinoma	19077451	CNVD
Chronic lymphocytic leukemia	20421269	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:150 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3378400-3390400	Weak transcription	Ovary	ovary
2	chr4:3386200-3390000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr4:3386200-3391400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr4:3386400-3390800	Enhancers	Fetal Lung	lung
5	chr4:3386400-3391200	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr4:3386600-3390800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr4:3386600-3392400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr4:3386600-3393800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr4:3386800-3393600	Enhancers	H1 Cell Line	embryonic stem cell
10	chr4:3386800-3393600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr4:3386800-3395800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr4:3387400-3389800	Weak transcription	Fetal Intestine Large	intestine
13	chr4:3387600-3390600	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr4:3387600-3390600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr4:3387600-3392600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr4:3387800-3389800	Weak transcription	Primary T cells from cord blood	blood
17	chr4:3387800-3389800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr4:3387800-3391000	Active TSS	Esophagus	oesophagus
19	chr4:3388000-3390200	Active TSS	HMEC	breast
20	chr4:3388000-3394400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr4:3388200-3389800	Enhancers	Brain Substantia Nigra	brain
22	chr4:3388400-3390000	Enhancers	Fetal Kidney	kidney
23	chr4:3388400-3391200	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr4:3388400-3392000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
25	chr4:3388400-3393600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr4:3388600-3389800	Enhancers	Brain Inferior Temporal Lobe	brain
27	chr4:3388600-3390000	Enhancers	Left Ventricle	heart
28	chr4:3388600-3392000	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr4:3388600-3392400	Enhancers	Fetal Muscle Trunk	muscle
30	chr4:3388600-3394400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr4:3388800-3389800	Enhancers	iPS-20b Cell Line	embryonic stem cell
32	chr4:3388800-3389800	Enhancers	Right Ventricle	heart
33	chr4:3388800-3389800	Enhancers	Thymus	Thymus
34	chr4:3388800-3390000	Enhancers	Gastric	stomach
35	chr4:3388800-3390000	Enhancers	Pancreas	Pancrea
36	chr4:3388800-3390200	Enhancers	H9 Cell Line	embryonic stem cell
37	chr4:3388800-3390200	Enhancers	Brain Angular Gyrus	brain
38	chr4:3388800-3390800	Enhancers	iPS-18 Cell Line	embryonic stem cell
39	chr4:3388800-3391200	Enhancers	Fetal Intestine Small	intestine
40	chr4:3388800-3391400	Enhancers	Fetal Heart	heart
41	chr4:3388800-3391600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr4:3388800-3391800	Enhancers	Fetal Muscle Leg	muscle
43	chr4:3388800-3392000	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr4:3388800-3392600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
45	chr4:3388800-3392600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr4:3388800-3392800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr4:3388800-3394400	Enhancers	HUES48 Cell Line	embryonic stem cell
48	chr4:3389000-3390000	Active TSS	Rectal Mucosa Donor 29	rectum
49	chr4:3389000-3390600	Enhancers	Fetal Brain Male	brain
50	chr4:3389000-3390600	Flanking Active TSS	GM12878-XiMat	blood

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