Variant report

Variant	esv1816415
Chromosome Location	chr4:119331323-119387097
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	chr4:119340543-119341192	GM12878	blood:	n/a	chr4:119340900-119340911
2	BATF	chr4:119349910-119350272	GM12878	blood:	n/a	n/a
3	BATF	chr4:119340637-119341181	GM12878	blood:	n/a	chr4:119340900-119340911
4	BATF	chr4:119346684-119346850	GM12878	blood:	n/a	n/a
5	BCL11A	chr4:119348069-119348301	GM12878	blood:	n/a	n/a
6	BCL11A	chr4:119340615-119341149	GM12878	blood:	n/a	chr4:119340900-119340909
7	BCL11A	chr4:119347436-119347664	GM12878	blood:	n/a	n/a
8	BCL11A	chr4:119349658-119349869	GM12878	blood:	n/a	n/a
9	BCL11A	chr4:119340729-119341128	GM12878	blood:	n/a	chr4:119340900-119340909
10	BCL11A	chr4:119346839-119347055	GM12878	blood:	n/a	n/a
11	BCL11A	chr4:119357419-119357683	GM12878	blood:	n/a	n/a
12	BCL11A	chr4:119345259-119345545	GM12878	blood:	n/a	n/a
13	BCL11A	chr4:119366080-119366250	GM12878	blood:	n/a	n/a
14	BCL3	chr4:119382599-119382899	GM12878	blood:	n/a	n/a
15	CEBPB	chr4:119337044-119337239	IMR90	lung:	n/a	n/a
16	CEBPB	chr4:119340970-119341155	Hela-S3	cervix:	n/a	chr4:119340996-119341007 chr4:119341094-119341111 chr4:119340996-119341009
17	CEBPB	chr4:119338475-119338816	IMR90	lung:	n/a	n/a
18	CEBPB	chr4:119340977-119341100	IMR90	lung:	n/a	chr4:119340996-119341007 chr4:119340996-119341009
19	CEBPB	chr4:119331341-119331666	IMR90	lung:	n/a	n/a
20	CEBPB	chr4:119340964-119341126	HepG2	liver:	n/a	chr4:119340996-119341007 chr4:119341094-119341111 chr4:119340996-119341009
21	CEBPB	chr4:119382583-119382910	IMR90	lung:	n/a	chr4:119382722-119382733
22	CEBPB	chr4:119376054-119376279	IMR90	lung:	n/a	n/a
23	CEBPB	chr4:119351771-119351934	K562	blood:	n/a	n/a
24	CHD2	chr4:119345423-119345555	H1-hESC	embryonic stem cell:	n/a	n/a
25	CTCF	chr4:119345380-119345530	HRE	kidney:	n/a	n/a
26	CTCF	chr4:119345280-119345430	GM12878	blood:	n/a	n/a
27	CTCF	chr4:119345320-119345470	HRPEpiC	eye:	n/a	n/a
28	CTCF	chr4:119353280-119353430	GM12874	blood:	n/a	n/a
29	CTCF	chr4:119371579-119371615	H1-hESC	embryonic stem cell:	n/a	n/a
30	CTCF	chr4:119345317-119345503	GM19239	blood:	n/a	n/a
31	CTCF	chr4:119345300-119345450	HCFaa	heart:	n/a	n/a
32	CTCF	chr4:119345320-119345470	HFF	foreskin:	n/a	n/a
33	CTCF	chr4:119353279-119353285	MCF-7	breast:	n/a	n/a
34	CTCF	chr4:119349722-119349782	Kidney_OC	kidney:	n/a	n/a
35	CTCF	chr4:119345300-119345450	GM12864	blood:	n/a	n/a
36	CTCF	chr4:119344960-119345110	HBMEC	blood vessel:	n/a	n/a
37	CTCF	chr4:119345320-119345470	BE2_C	brain:	n/a	n/a
38	CTCF	chr4:119345320-119345470	GM12868	blood:	n/a	n/a
39	CTCF	chr4:119345320-119345470	GM12869	blood:	n/a	n/a
40	CTCF	chr4:119345320-119345470	HAc	cerebellar:	n/a	n/a
41	CTCF	chr4:119345320-119345470	GM12866	blood:	n/a	n/a
42	CTCF	chr4:119345380-119345530	HMEC	breast:	n/a	n/a
43	CTCF	chr4:119345320-119345470	HFF-Myc	foreskin:	n/a	n/a
44	CTCF	chr4:119353300-119353450	GM12872	blood:	n/a	n/a
45	CTCF	chr4:119345212-119345645	A549	lung:	n/a	n/a
46	CTCF	chr4:119345560-119345710	GM12873	blood:	n/a	n/a
47	CTCF	chr4:119345320-119345470	NHDF-neo	bronchial:	n/a	n/a
48	CTCF	chr4:119345314-119345496	HUVEC	blood vessel:	n/a	n/a
49	CTCF	chr4:119345293-119345604	H1-hESC	embryonic stem cell:	n/a	n/a
50	CTCF	chr4:119345380-119345530	WERI-Rb-1	eye:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:119198536..119201399-chr4:119334515..119337557,3	MCF-7	breast:
2	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: 913 )
Associated
traits (count: 76 )

Variant overlapped rSNPs/rCNVs (count:913 , 50 per page) page: 1 2 3 4 5 6 7 ... 19

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs540835839	chr4:119331334-119331335	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs560772925	chr4:119331362-119331363	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs10518293	chr4:119331363-119331364	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
4	rs34867697	chr4:119331374-119331375	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs549894542	chr4:119331379-119331380	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs569703482	chr4:119331392-119331393	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs575858946	chr4:119331511-119331512	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs184762232	chr4:119331533-119331534	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs56410164	chr4:119331625-119331626	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
10	rs566200664	chr4:119331643-119331644	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs11933005	chr4:119331671-119331672	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
12	rs4834683	chr4:119331723-119331724	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
13	rs568705542	chr4:119331739-119331740	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs536344063	chr4:119331756-119331757	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs556341221	chr4:119331811-119331812	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs11942152	chr4:119331857-119331858	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
17	rs544639593	chr4:119331859-119331860	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs558540959	chr4:119331947-119331948	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs186613471	chr4:119331955-119331956	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs74336493	chr4:119331983-119331984	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs191402060	chr4:119331987-119331988	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs138943058	chr4:119331989-119331990	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs143358357	chr4:119332021-119332022	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs564666253	chr4:119332038-119332039	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs72903300	chr4:119332083-119332084	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs184880140	chr4:119332111-119332112	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs372831403	chr4:119332163-119332164	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs11943179	chr4:119332179-119332180	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
29	rs34498795	chr4:119332231-119332232	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs376439572	chr4:119332241-119332242	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs527379456	chr4:119332271-119332272	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs566086671	chr4:119332273-119332274	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs574586511	chr4:119332279-119332280	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs6813677	chr4:119332290-119332291	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
35	rs189762419	chr4:119332309-119332310	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs6813853	chr4:119332330-119332331	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
37	rs537596902	chr4:119332339-119332340	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs530007061	chr4:119332344-119332345	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs549780819	chr4:119332346-119332347	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs551207772	chr4:119332350-119332351	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs112591893	chr4:119332408-119332409	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs181374392	chr4:119332416-119332417	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs118041351	chr4:119332422-119332423	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs185051636	chr4:119332427-119332428	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs147114673	chr4:119332469-119332470	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs55914305	chr4:119332527-119332528	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs71608369	chr4:119332549-119332550	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs149395401	chr4:119332552-119332553	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs569851274	chr4:119332556-119332557	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs397723558	chr4:119332559-119332560	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:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:119325800-119334800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr4:119331000-119331600	Enhancers	HMEC	breast
3	chr4:119331000-119332000	Enhancers	NHEK	skin
4	chr4:119331200-119331600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr4:119331200-119331600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr4:119331200-119331600	Enhancers	NH-A	brain
7	chr4:119331200-119331800	Enhancers	Muscle Satellite Cultured Cells	--
8	chr4:119331200-119332000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr4:119331200-119332000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr4:119331200-119332000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr4:119331600-119337400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr4:119334800-119335000	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr4:119334800-119335000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr4:119335000-119336800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr4:119336800-119337000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr4:119337400-119339200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr4:119337600-119339400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr4:119338000-119339200	Enhancers	HMEC	breast
19	chr4:119338000-119339400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr4:119338000-119339400	Enhancers	NHEK	skin
21	chr4:119338200-119338600	Enhancers	Muscle Satellite Cultured Cells	--
22	chr4:119338400-119338600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr4:119338400-119338800	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr4:119338400-119338800	Enhancers	Osteobl	bone
25	chr4:119338400-119339000	Enhancers	HSMMtube	muscle
26	chr4:119338400-119339400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr4:119338600-119339000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr4:119338600-119339200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr4:119338600-119339200	Enhancers	Liver	Liver
30	chr4:119338600-119339800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr4:119338800-119339200	Bivalent Enhancer	Osteobl	bone
32	chr4:119339200-119339400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr4:119339200-119340600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr4:119340600-119340800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr4:119340600-119341000	Active TSS	Osteobl	bone
36	chr4:119340800-119345400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr4:119344200-119345600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr4:119345400-119345600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr4:119345400-119345800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr4:119345400-119345800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr4:119345400-119345800	Enhancers	Dnd41	blood
42	chr4:119345600-119345800	Enhancers	ES-I3 Cell Line	embryonic stem cell
43	chr4:119346200-119347000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr4:119355000-119356200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr4:119355200-119355600	Enhancers	Cortex derived primary cultured neurospheres	brain
46	chr4:119356000-119356800	Enhancers	Fetal Muscle Leg	muscle
47	chr4:119363400-119363800	Enhancers	ES-I3 Cell Line	embryonic stem cell
48	chr4:119363400-119363800	Enhancers	HUES6 Cell Line	embryonic stem cell
49	chr4:119378600-119379400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr4:119382400-119382800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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