Variant report

Variant	esv1824368
Chromosome Location	chr4:119340220-119387297
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	BATF	chr4:119340637-119341181	GM12878	blood:	n/a	chr4:119340900-119340911
2	BATF	chr4:119346684-119346850	GM12878	blood:	n/a	n/a
3	BATF	chr4:119349910-119350272	GM12878	blood:	n/a	n/a
4	BATF	chr4:119340543-119341192	GM12878	blood:	n/a	chr4:119340900-119340911
5	BCL11A	chr4:119345259-119345545	GM12878	blood:	n/a	n/a
6	BCL11A	chr4:119357419-119357683	GM12878	blood:	n/a	n/a
7	BCL11A	chr4:119349658-119349869	GM12878	blood:	n/a	n/a
8	BCL11A	chr4:119346839-119347055	GM12878	blood:	n/a	n/a
9	BCL11A	chr4:119366080-119366250	GM12878	blood:	n/a	n/a
10	BCL11A	chr4:119348069-119348301	GM12878	blood:	n/a	n/a
11	BCL11A	chr4:119347436-119347664	GM12878	blood:	n/a	n/a
12	BCL11A	chr4:119340615-119341149	GM12878	blood:	n/a	chr4:119340900-119340909
13	BCL11A	chr4:119340729-119341128	GM12878	blood:	n/a	chr4:119340900-119340909
14	BCL3	chr4:119382599-119382899	GM12878	blood:	n/a	n/a
15	CEBPB	chr4:119340970-119341155	Hela-S3	cervix:	n/a	chr4:119340996-119341007 chr4:119341094-119341111 chr4:119340996-119341009
16	CEBPB	chr4:119340977-119341100	IMR90	lung:	n/a	chr4:119340996-119341007 chr4:119340996-119341009
17	CEBPB	chr4:119376054-119376279	IMR90	lung:	n/a	n/a
18	CEBPB	chr4:119340964-119341126	HepG2	liver:	n/a	chr4:119340996-119341007 chr4:119341094-119341111 chr4:119340996-119341009
19	CEBPB	chr4:119382583-119382910	IMR90	lung:	n/a	chr4:119382722-119382733
20	CEBPB	chr4:119351771-119351934	K562	blood:	n/a	n/a
21	CHD2	chr4:119345423-119345555	H1-hESC	embryonic stem cell:	n/a	n/a
22	CTCF	chr4:119353160-119353310	HEK293	kidney:	n/a	n/a
23	CTCF	chr4:119345270-119345538	Fibrobl	skin:	n/a	n/a
24	CTCF	chr4:119368079-119368248	K562	blood:	n/a	n/a
25	CTCF	chr4:119371545-119371653	LNCaP	prostate:	n/a	n/a
26	CTCF	chr4:119345300-119345450	AG09319	gingival:	n/a	n/a
27	CTCF	chr4:119371523-119371662	LNCaP	prostate:	n/a	n/a
28	CTCF	chr4:119353280-119353430	GM12874	blood:	n/a	n/a
29	CTCF	chr4:119345300-119345450	AG09309	skin:	n/a	n/a
30	CTCF	chr4:119345320-119345470	GM12871	blood:	n/a	n/a
31	CTCF	chr4:119353180-119353330	GM12869	blood:	n/a	n/a
32	CTCF	chr4:119345276-119345547	Medullo	brain:	n/a	n/a
33	CTCF	chr4:119345320-119345470	GM12864	blood:	n/a	n/a
34	CTCF	chr4:119345280-119345430	GM12878	blood:	n/a	n/a
35	CTCF	chr4:119345306-119345491	Hela-S3	cervix:	n/a	n/a
36	CTCF	chr4:119345320-119345470	HVMF	connective:	n/a	n/a
37	CTCF	chr4:119345300-119345450	WERI-Rb-1	eye:	n/a	n/a
38	CTCF	chr4:119345380-119345530	GM12874	blood:	n/a	n/a
39	CTCF	chr4:119345380-119345530	BJ	skin:	n/a	n/a
40	CTCF	chr4:119353300-119353450	GM12872	blood:	n/a	n/a
41	CTCF	chr4:119371579-119371615	H1-hESC	embryonic stem cell:	n/a	n/a
42	CTCF	chr4:119345500-119345650	SK-N-SH_RA	brain:	n/a	n/a
43	CTCF	chr4:119345320-119345470	GM12866	blood:	n/a	n/a
44	CTCF	chr4:119345300-119345450	SK-N-SH_RA	brain:	n/a	n/a
45	CTCF	chr4:119345320-119345470	NB4	blood:	n/a	n/a
46	CTCF	chr4:119345380-119345530	HMEC	breast:	n/a	n/a
47	CTCF	chr4:119345380-119345530	HRE	kidney:	n/a	n/a
48	CTCF	chr4:119371640-119371790	WERI-Rb-1	eye:	n/a	n/a
49	CTCF	chr4:119345320-119345470	HA-sp	spinal cord:	n/a	n/a
50	CTCF	chr4:119345290-119345507	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:119199281..119200962-chr4:119368800..119371509,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NDST3-3	chr4:119349734-119350000	XLOC_003661
2	lnc-NDST3-3	chr4:119350138-119350584	XLOC_003661
3	lnc-NDST3-3	chr4:119348948-119349038	XLOC_003661

Variant related genes	Relation type
CEP170P1	TF binding region
ENSG00000269893	chromatin interactions

Extended variants
information (count: 565 )
Associated
traits (count: 76 )

Variant overlapped rSNPs/rCNVs (count:565 , 50 per page) page: 1 2 3 4 5 6 7 ... 12

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs4001536	chr4:119340269-119340270	Weak transcription	n/a	n/a	Overlapped CNVs	mRNA abundance
2	rs536136800	chr4:119340287-119340288	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs549321029	chr4:119340318-119340319	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs569387784	chr4:119340321-119340322	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs557098596	chr4:119340399-119340400	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs570594333	chr4:119340403-119340404	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs200318414	chr4:119340470-119340471	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs71608374	chr4:119340504-119340505	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
9	rs185721854	chr4:119340511-119340512	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs71608375	chr4:119340514-119340515	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
11	rs573383062	chr4:119340518-119340519	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs535811268	chr4:119340553-119340554	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs1843662	chr4:119340679-119340680	Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
14	rs576989188	chr4:119340691-119340692	Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
15	rs4001513	chr4:119340692-119340693	Enhancers Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
16	rs544615123	chr4:119340718-119340719	Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
17	rs200844818	chr4:119340740-119340741	Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
18	rs202009712	chr4:119340785-119340786	Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
19	rs4001514	chr4:119340806-119340807	Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
20	rs3879779	chr4:119340827-119340828	Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
21	rs577866754	chr4:119340863-119340864	Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
22	rs540433388	chr4:119340874-119340875	Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
23	rs558983868	chr4:119340901-119340902	Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
24	rs539485747	chr4:119340912-119340913	Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
25	rs3879780	chr4:119340936-119340937	Weak transcription Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
26	rs3879781	chr4:119340937-119340938	Weak transcription Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
27	rs192012028	chr4:119340942-119340943	Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
28	rs550647264	chr4:119340963-119340964	Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
29	rs570763228	chr4:119340991-119340992	Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
30	rs201615377	chr4:119341009-119341010	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs539602320	chr4:119341029-119341030	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs546829813	chr4:119341037-119341038	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs566940201	chr4:119341040-119341041	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs535601695	chr4:119341059-119341060	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs555714573	chr4:119341143-119341144	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs575592310	chr4:119341151-119341152	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs3870828	chr4:119341156-119341157	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs538529656	chr4:119341163-119341164	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs558124367	chr4:119341178-119341179	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs577928740	chr4:119341241-119341242	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs113971542	chr4:119341327-119341328	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs4001521	chr4:119341364-119341365	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs540394563	chr4:119341382-119341383	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs144803899	chr4:119341585-119341586	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs560336899	chr4:119341606-119341607	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs71608377	chr4:119341610-119341611	Weak transcription	n/a	n/a	Overlapped CNVs	mRNA abundance
47	rs541595644	chr4:119341623-119341624	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs114321375	chr4:119341663-119341664	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs530377322	chr4:119341792-119341793	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs550560351	chr4:119341803-119341804	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:76)

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
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Melanoma	18172304	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Breast cancer	17603634	CNVD
Esophageal squamous carcinoma	18350619	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
Myelodysplastic syndrome	21251322	CNVD
Lung cancer	18438408	CNVD
Cancer	22429812	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Cancer	21183584	CNVD
primary effusion lymphomas	17116491	CNVD
Splenic marginal zone lymphoma	21957467	CNVD
Breast cancer	17133270	CNVD
Colorectal cancer	20459617	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Congenital anomalies of the kidney and urinary tract	20505237	CNVD
Breast cancer	17393978	CNVD
Esophageal cancer	21851588	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Colorectal cancer	16272173	CNVD
Testicular germ cell tumor	18059402	CNVD
Ovarian cancer	22174824	CNVD
Cutaneous T-cell lymphoma	21881587	CNVD
Myelofibrosis	22110671	CNVD
Neuroblastoma	21899760	CNVD
small cell lung cancer	20016488	CNVD
Renal cell carcinoma	18194544	CNVD
Autism	19246517	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
Breast cancer	22522925	CNVD
early-passage human iPS cells	21368824	CNVD
Pancreatic cancer	17952125	CNVD
Non-syndromic sensorineural hearing loss	19587683	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:119339200-119340600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr4:119340600-119340800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr4:119340600-119341000	Active TSS	Osteobl	bone
4	chr4:119340800-119345400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr4:119344200-119345600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr4:119345400-119345600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr4:119345400-119345800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr4:119345400-119345800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr4:119345400-119345800	Enhancers	Dnd41	blood
10	chr4:119345600-119345800	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr4:119346200-119347000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr4:119355000-119356200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr4:119355200-119355600	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr4:119356000-119356800	Enhancers	Fetal Muscle Leg	muscle
15	chr4:119363400-119363800	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr4:119363400-119363800	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr4:119378600-119379400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr4:119382400-119382800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr4:119386800-119387200	Enhancers	NHDF-Ad	bronchial
20	chr4:119386800-119387400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr4:119387200-119387600	Weak transcription	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links