Variant report

Variant	esv3487185
Chromosome Location	chr4:1289651-1290242
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	EBF1	chr4:1289571-1289819	GM12878	blood:	n/a	n/a
2	MYC	chr4:1289798-1289801	MCF-7	breast:	n/a	n/a
3	MYC	chr4:1289840-1289855	MCF-7	breast:	n/a	n/a
4	POLR2A	chr4:1289669-1289795	GM12878	blood:	n/a	n/a
5	POLR2A	chr4:1289624-1289825	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr4:1289931-1289990	HepG2	liver:	n/a	n/a
7	POLR2A	chr4:1290153-1290458	K562	blood:	n/a	n/a
8	POLR2A	chr4:1289803-1290003	K562	blood:	n/a	n/a
9	POLR2A	chr4:1289945-1290008	ProgFib	skin:	n/a	n/a
10	POLR2A	chr4:1288600-1289797	K562	blood:	n/a	n/a
11	POLR2A	chr4:1289632-1290130	K562	blood:	n/a	n/a
12	ZEB1	chr4:1290142-1290365	GM12878	blood:	n/a	chr4:1290196-1290203 chr4:1290291-1290300
13	ZEB1	chr4:1289532-1289798	GM12878	blood:	n/a	n/a
14	ZEB1	chr4:1290040-1290491	GM12878	blood:	n/a	chr4:1290196-1290203 chr4:1290291-1290300
15	ZEB1	chr4:1289153-1289818	GM12878	blood:	n/a	chr4:1289484-1289493

No.	Distal block	Cell Line	Cell type
1	chr4:1289122..1291329-chr4:1338444..1340407,2	MCF-7	breast:
2	chr4:1236833..1250005-chr4:1276188..1292579,54	MCF-7	breast:
3	chr4:1288933..1290698-chr4:1333775..1336445,2	K562	blood:
4	chr4:1036618..1039246-chr4:1287884..1290247,2	K562	blood:
5	chr4:1287434..1290416-chr4:1342936..1345119,2	K562	blood:
6	chr4:1241391..1244976-chr4:1289369..1292052,3	MCF-7	breast:

Variant related genes	Relation type
MAEA	TF binding region
ENSG00000196810	chromatin interactions
ENSG00000159692	chromatin interactions

Extended variants
information (count: 29 )
Associated
traits (count: 64 )

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	rs114981738	chr4:1289673-1289674	Weak transcription Genic enhancers Strong transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
2	rs193043147	chr4:1289736-1289737	Weak transcription Genic enhancers Strong transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
3	rs185305831	chr4:1289739-1289740	Weak transcription Genic enhancers Strong transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
4	rs137969700	chr4:1289758-1289759	Weak transcription Genic enhancers Strong transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
5	rs540482132	chr4:1289764-1289765	Weak transcription Genic enhancers Strong transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
6	rs376728033	chr4:1289773-1289774	Weak transcription Genic enhancers Strong transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
7	rs565336180	chr4:1289813-1289814	Weak transcription Genic enhancers Strong transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
8	rs369002852	chr4:1289888-1289889	Weak transcription Genic enhancers Strong transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
9	rs531988706	chr4:1289920-1289921	Weak transcription Genic enhancers Strong transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
10	rs550208315	chr4:1289923-1289924	Weak transcription Genic enhancers Strong transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
11	rs565248140	chr4:1289940-1289941	Weak transcription Genic enhancers Strong transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
12	rs532586715	chr4:1289944-1289945	Weak transcription Genic enhancers Strong transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
13	rs71168821	chr4:1289964-1289965	Weak transcription Genic enhancers Strong transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
14	rs201628544	chr4:1289975-1289976	Weak transcription Genic enhancers Strong transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
15	rs547893103	chr4:1290010-1290011	Weak transcription Genic enhancers Strong transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
16	rs369697185	chr4:1290089-1290090	Weak transcription Genic enhancers Strong transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
17	rs550917874	chr4:1290137-1290138	Weak transcription Genic enhancers Strong transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
18	rs562777980	chr4:1290154-1290155	Weak transcription Genic enhancers Strong transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
19	rs66879211	chr4:1290180-1290181	Weak transcription Genic enhancers Strong transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
20	rs548126339	chr4:1290189-1290190	Weak transcription Genic enhancers Strong transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
21	rs72501965	chr4:1290191-1290192	Weak transcription Genic enhancers Strong transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
22	rs533698602	chr4:1290195-1290196	Weak transcription Genic enhancers Strong transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
23	rs147314573	chr4:1290208-1290209	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
24	rs189771196	chr4:1290209-1290210	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
25	rs71168822	chr4:1290211-1290212	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
26	rs570497038	chr4:1290227-1290228	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
27	rs376902248	chr4:1290235-1290236	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
28	rs373066546	chr4:1290238-1290239	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
29	rs73069986	chr4:1290241-1290242	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a

Variant related diseases (count:64)

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
Breast cancer	20932292	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD
Type 2 diabetes	21754918	CNVD

Chromatin state (count:178 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:1284600-1290200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:1285200-1290200	Weak transcription	Aorta	Aorta
3	chr4:1285200-1293800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr4:1285200-1303400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:1285400-1290200	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr4:1285400-1290600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr4:1285400-1291200	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr4:1285400-1291200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr4:1285400-1293400	Weak transcription	A549	lung
10	chr4:1285400-1294200	Weak transcription	HSMMtube	muscle
11	chr4:1285400-1294200	Weak transcription	HUVEC	blood vessel
12	chr4:1285400-1302400	Weak transcription	Fetal Kidney	kidney
13	chr4:1285600-1290200	Weak transcription	Fetal Lung	lung
14	chr4:1285600-1290600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr4:1285600-1291400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr4:1285800-1296000	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr4:1285800-1302200	Weak transcription	NHDF-Ad	bronchial
18	chr4:1286000-1295200	Strong transcription	Thymus	Thymus
19	chr4:1286200-1290200	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr4:1286200-1290800	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr4:1286200-1291400	Weak transcription	Hela-S3	cervix
22	chr4:1286200-1293400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr4:1286200-1299200	Strong transcription	Fetal Intestine Small	intestine
24	chr4:1286200-1302400	Weak transcription	Fetal Brain Male	brain
25	chr4:1286400-1290600	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr4:1286400-1299000	Weak transcription	Small Intestine	intestine
27	chr4:1286600-1290200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr4:1286600-1290200	Weak transcription	NHLF	lung
29	chr4:1287200-1290400	Enhancers	Right Atrium	heart
30	chr4:1287400-1289800	Genic enhancers	Fetal Muscle Trunk	muscle
31	chr4:1287400-1291800	Genic enhancers	Gastric	stomach
32	chr4:1287400-1292000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr4:1287400-1294600	Genic enhancers	Spleen	Spleen
34	chr4:1287600-1290200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr4:1287600-1290400	Enhancers	HMEC	breast
36	chr4:1287600-1295200	Genic enhancers	Primary T cells fromperipheralblood	blood
37	chr4:1287800-1290000	Weak transcription	Fetal Brain Female	brain
38	chr4:1287800-1290800	Genic enhancers	Right Ventricle	heart
39	chr4:1287800-1293400	Weak transcription	HSMM	muscle
40	chr4:1288000-1290200	Weak transcription	NHEK	skin
41	chr4:1288000-1291000	Weak transcription	HepG2	liver
42	chr4:1288000-1291200	Weak transcription	NH-A	brain
43	chr4:1288200-1290200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr4:1288200-1290200	Weak transcription	Dnd41	blood
45	chr4:1288200-1290400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr4:1288200-1290600	Weak transcription	Brain Substantia Nigra	brain
47	chr4:1288400-1290000	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr4:1288400-1290200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr4:1288400-1290200	Weak transcription	Primary B cells from peripheral blood	blood
50	chr4:1288400-1290600	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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