Variant report

Variant	esv1800375
Chromosome Location	chr4:119339003-119391798
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	chr4:119340543-119341192	GM12878	blood:	n/a	chr4:119340900-119340911
3	BATF	chr4:119346684-119346850	GM12878	blood:	n/a	n/a
4	BATF	chr4:119349910-119350272	GM12878	blood:	n/a	n/a
5	BCL11A	chr4:119340615-119341149	GM12878	blood:	n/a	chr4:119340900-119340909
6	BCL11A	chr4:119366080-119366250	GM12878	blood:	n/a	n/a
7	BCL11A	chr4:119357419-119357683	GM12878	blood:	n/a	n/a
8	BCL11A	chr4:119340729-119341128	GM12878	blood:	n/a	chr4:119340900-119340909
9	BCL11A	chr4:119347436-119347664	GM12878	blood:	n/a	n/a
10	BCL11A	chr4:119349658-119349869	GM12878	blood:	n/a	n/a
11	BCL11A	chr4:119348069-119348301	GM12878	blood:	n/a	n/a
12	BCL11A	chr4:119345259-119345545	GM12878	blood:	n/a	n/a
13	BCL11A	chr4:119346839-119347055	GM12878	blood:	n/a	n/a
14	BCL3	chr4:119382599-119382899	GM12878	blood:	n/a	n/a
15	CEBPB	chr4:119340964-119341126	HepG2	liver:	n/a	chr4:119340996-119341007 chr4:119341094-119341111 chr4:119340996-119341009
16	CEBPB	chr4:119351771-119351934	K562	blood:	n/a	n/a
17	CEBPB	chr4:119340977-119341100	IMR90	lung:	n/a	chr4:119340996-119341007 chr4:119340996-119341009
18	CEBPB	chr4:119340970-119341155	Hela-S3	cervix:	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	chr4:119376054-119376279	IMR90	lung:	n/a	n/a
21	CHD2	chr4:119345423-119345555	H1-hESC	embryonic stem cell:	n/a	n/a
22	CTCF	chr4:119373759-119373852	Kidney_OC	kidney:	n/a	n/a
23	CTCF	chr4:119353215-119353400	LNCaP	prostate:	n/a	n/a
24	CTCF	chr4:119345380-119345530	HMF	breast:	n/a	n/a
25	CTCF	chr4:119386938-119386954	Pancreas_OC	pancreas:	n/a	n/a
26	CTCF	chr4:119345380-119345530	HL-60	blood:	n/a	n/a
27	CTCF	chr4:119345400-119345670	NHEK	skin:	n/a	n/a
28	CTCF	chr4:119353200-119353350	AG04449	skin:	n/a	n/a
29	CTCF	chr4:119345380-119345530	GM12865	blood:	n/a	n/a
30	CTCF	chr4:119345300-119345450	HEK293	kidney:	n/a	n/a
31	CTCF	chr4:119345275-119345548	A549	lung:	n/a	n/a
32	CTCF	chr4:119345320-119345610	WI-38	lung:	n/a	n/a
33	CTCF	chr4:119353279-119353285	MCF-7	breast:	n/a	n/a
34	CTCF	chr4:119345300-119345450	HEEpiC	esophagus:	n/a	n/a
35	CTCF	chr4:119353240-119353390	GM12871	blood:	n/a	n/a
36	CTCF	chr4:119345380-119345530	HCPEpiC	choroid plexus:	n/a	n/a
37	CTCF	chr4:119345300-119345450	HUVEC	blood vessel:	n/a	n/a
38	CTCF	chr4:119345380-119345530	HRPEpiC	eye:	n/a	n/a
39	CTCF	chr4:119345380-119345530	GM12873	blood:	n/a	n/a
40	CTCF	chr4:119353285-119353314	K562	blood:	n/a	n/a
41	CTCF	chr4:119345320-119345470	GM12866	blood:	n/a	n/a
42	CTCF	chr4:119345230-119345616	IMR90	lung:	n/a	n/a
43	CTCF	chr4:119345264-119345549	NHEK	skin:	n/a	n/a
44	CTCF	chr4:119345380-119345530	HBMEC	blood vessel:	n/a	n/a
45	CTCF	chr4:119345380-119345530	AG09319	gingival:	n/a	n/a
46	CTCF	chr4:119345365-119345439	Spleen_OC	spleen:	n/a	n/a
47	CTCF	chr4:119353291-119353306	MCF-7	breast:	n/a	n/a
48	CTCF	chr4:119388286-119388341	MCF-7	breast:	n/a	n/a
49	CTCF	chr4:119345320-119345470	GM12867	blood:	n/a	n/a
50	CTCF	chr4:119345280-119345430	GM12864	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: 756 )
Associated
traits (count: 76 )

Variant overlapped rSNPs/rCNVs (count:756 , 50 per page) page: 1 2 3 4 5 6 7 ... 16

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs528390995	chr4:119339045-119339046	Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
2	rs535436855	chr4:119339058-119339059	Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
3	rs370944618	chr4:119339133-119339134	Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
4	rs188393653	chr4:119339166-119339167	Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
5	rs541699182	chr4:119339181-119339182	Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
6	rs1828857	chr4:119339182-119339183	Enhancers Bivalent Enhancer	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs1808022	chr4:119339208-119339209	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
8	rs556894418	chr4:119339222-119339223	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs1828856	chr4:119339227-119339228	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
10	rs530909226	chr4:119339336-119339337	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs3896922	chr4:119339345-119339346	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs546352195	chr4:119339367-119339368	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs553393316	chr4:119339458-119339459	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs573320721	chr4:119339484-119339485	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs542246312	chr4:119339499-119339500	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs4103597	chr4:119339515-119339516	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs3879776	chr4:119339569-119339570	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs71608371	chr4:119339691-119339692	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs531124020	chr4:119339767-119339768	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs544761463	chr4:119339913-119339914	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs564550691	chr4:119339923-119339924	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs532064782	chr4:119339950-119339951	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs4103612	chr4:119340054-119340055	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs565335863	chr4:119340062-119340063	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs570529012	chr4:119340064-119340065	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs528034062	chr4:119340077-119340078	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs533190988	chr4:119340139-119340140	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs574863506	chr4:119340163-119340164	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs181218832	chr4:119340164-119340165	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs4001535	chr4:119340192-119340193	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs568311096	chr4:119340203-119340204	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs4001536	chr4:119340269-119340270	Weak transcription	n/a	n/a	Overlapped CNVs	mRNA abundance
33	rs536136800	chr4:119340287-119340288	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs549321029	chr4:119340318-119340319	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs569387784	chr4:119340321-119340322	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs557098596	chr4:119340399-119340400	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs570594333	chr4:119340403-119340404	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs200318414	chr4:119340470-119340471	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs71608374	chr4:119340504-119340505	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
40	rs185721854	chr4:119340511-119340512	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs71608375	chr4:119340514-119340515	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
42	rs573383062	chr4:119340518-119340519	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs535811268	chr4:119340553-119340554	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs1843662	chr4:119340679-119340680	Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
45	rs576989188	chr4:119340691-119340692	Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
46	rs4001513	chr4:119340692-119340693	Enhancers Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
47	rs544615123	chr4:119340718-119340719	Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
48	rs200844818	chr4:119340740-119340741	Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
49	rs202009712	chr4:119340785-119340786	Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
50	rs4001514	chr4:119340806-119340807	Weak transcription Active TSS	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:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:119337400-119339200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr4:119337600-119339400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr4:119338000-119339200	Enhancers	HMEC	breast
4	chr4:119338000-119339400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr4:119338000-119339400	Enhancers	NHEK	skin
6	chr4:119338400-119339400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr4:119338600-119339200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr4:119338600-119339200	Enhancers	Liver	Liver
9	chr4:119338600-119339800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr4:119338800-119339200	Bivalent Enhancer	Osteobl	bone
11	chr4:119339200-119339400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr4:119339200-119340600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr4:119340600-119340800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr4:119340600-119341000	Active TSS	Osteobl	bone
15	chr4:119340800-119345400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr4:119344200-119345600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr4:119345400-119345600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr4:119345400-119345800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr4:119345400-119345800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr4:119345400-119345800	Enhancers	Dnd41	blood
21	chr4:119345600-119345800	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr4:119346200-119347000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr4:119355000-119356200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr4:119355200-119355600	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr4:119356000-119356800	Enhancers	Fetal Muscle Leg	muscle
26	chr4:119363400-119363800	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr4:119363400-119363800	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr4:119378600-119379400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr4:119382400-119382800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr4:119386800-119387200	Enhancers	NHDF-Ad	bronchial
31	chr4:119386800-119387400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr4:119387200-119387600	Weak transcription	NHDF-Ad	bronchial
33	chr4:119387400-119387800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr4:119387600-119388200	Enhancers	NHDF-Ad	bronchial
35	chr4:119387600-119390200	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr4:119387800-119388000	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr4:119387800-119388200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr4:119387800-119388200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr4:119387800-119388800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr4:119388000-119388800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr4:119388000-119389800	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr4:119388200-119395000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr4:119389800-119390000	Flanking Bivalent TSS/Enh	Primary T helper 17 cells PMA-I stimulated	--
44	chr4:119389800-119390000	Enhancers	Pancreas	Pancrea
45	chr4:119389800-119390000	Enhancers	Skeletal Muscle Male	skeletal muscle

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