Variant report

Variant	nsv1014467
Chromosome Location	chr3:21985380-22008097
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	CEBPB	chr3:21996134-21996664	IMR90	lung:	n/a	n/a
2	CEBPB	chr3:21996174-21996533	Hela-S3	cervix:	n/a	n/a
3	CTCF	chr3:21998853-21998886	GM13976	blood:	n/a	n/a
4	CTCF	chr3:21996780-21996930	GM06990	blood:	n/a	n/a
5	CTCF	chr3:21988251-21988325	LNCaP	prostate:	n/a	n/a
6	CTCF	chr3:22000640-22000790	HFF	foreskin:	n/a	n/a
7	E2F4	chr3:21995949-21996485	MCF10A-Er-Src	breast:	n/a	n/a
8	EBF1	chr3:21985565-21986097	GM12878	blood:	n/a	n/a
9	EP300	chr3:21996206-21996540	Hela-S3	cervix:	n/a	n/a
10	FOS	chr3:21996984-21997174	MCF10A-Er-Src	breast:	n/a	n/a
11	FOS	chr3:21996172-21996566	MCF10A-Er-Src	breast:	n/a	n/a
12	FOS	chr3:21996203-21996529	MCF10A-Er-Src	breast:	n/a	n/a
13	FOS	chr3:21995955-21996602	MCF10A-Er-Src	breast:	n/a	n/a
14	FOS	chr3:21996970-21997170	MCF10A-Er-Src	breast:	n/a	n/a
15	FOS	chr3:22004212-22004269	MCF10A-Er-Src	breast:	n/a	n/a
16	FOS	chr3:21996160-21996599	MCF10A-Er-Src	breast:	n/a	n/a
17	GATA3	chr3:22000365-22000565	SH-SY5Y	brain:	n/a	n/a
18	MYC	chr3:21997082-21997236	MCF10A-Er-Src	breast:	n/a	n/a
19	MYC	chr3:21996171-21996576	MCF10A-Er-Src	breast:	n/a	n/a
20	MYC	chr3:21990003-21990164	MCF10A-Er-Src	breast:	n/a	n/a
21	POLR2A	chr3:22006564-22006566	MCF10A-Er-Src	breast:	n/a	n/a
22	POLR2A	chr3:21996952-21997212	MCF10A-Er-Src	breast:	n/a	n/a
23	POLR2A	chr3:21985652-21986170	PFSK-1	brain:	n/a	n/a
24	POLR2A	chr3:21990551-21990561	MCF10A-Er-Src	breast:	n/a	n/a
25	POLR2A	chr3:21995353-21995553	MCF10A-Er-Src	breast:	n/a	n/a
26	POLR2A	chr3:21986647-21986887	MCF10A-Er-Src	breast:	n/a	n/a
27	POLR2A	chr3:21999444-21999644	MCF10A-Er-Src	breast:	n/a	n/a
28	POLR2A	chr3:22002845-22002859	MCF10A-Er-Src	breast:	n/a	n/a
29	POLR2A	chr3:21986019-21986139	MCF10A-Er-Src	breast:	n/a	n/a
30	POLR2A	chr3:22001068-22001096	MCF10A-Er-Src	breast:	n/a	n/a
31	POLR2A	chr3:22007873-22008023	MCF10A-Er-Src	breast:	n/a	n/a
32	POLR2A	chr3:22006991-22007152	MCF10A-Er-Src	breast:	n/a	n/a
33	POLR2A	chr3:21988980-21988993	MCF-7	breast:	n/a	n/a
34	POLR2A	chr3:21985615-21986038	H1-neurons	neurons:	n/a	n/a
35	POLR2A	chr3:21987099-21987264	MCF10A-Er-Src	breast:	n/a	n/a
36	SIN3AK20	chr3:21985643-21986103	PFSK-1	brain:	n/a	n/a
37	SIN3AK20	chr3:21985760-21985914	PFSK-1	brain:	n/a	n/a
38	STAT3	chr3:21996244-21996528	MCF10A-Er-Src	breast:	n/a	n/a
39	STAT3	chr3:22006678-22006768	MCF10A-Er-Src	breast:	n/a	n/a
40	STAT3	chr3:21996169-21996574	MCF10A-Er-Src	breast:	n/a	n/a
41	STAT3	chr3:22002310-22002412	MCF10A-Er-Src	breast:	n/a	n/a
42	STAT3	chr3:21996958-21997168	MCF10A-Er-Src	breast:	n/a	n/a
43	STAT3	chr3:21999887-22000040	MCF10A-Er-Src	breast:	n/a	chr3:21999968-21999979
44	STAT3	chr3:21999563-21999682	MCF10A-Er-Src	breast:	n/a	n/a
45	STAT3	chr3:21996202-21996525	MCF10A-Er-Src	breast:	n/a	n/a
46	STAT3	chr3:21987154-21987318	MCF10A-Er-Src	breast:	n/a	n/a
47	STAT3	chr3:22004223-22004573	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:126141332..126144254-chr3:22001697..22003217,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-UBE2E2-2	chr3:22000324-22000415	ENSG00000223351
2	lnc-UBE2E2-2	chr3:21998631-21998684	ENSG00000223351
3	lnc-UBE2E2-2	chr3:22000324-22000415	ENSG00000223351
4	lnc-UBE2E2-2	chr3:21998628-21998684	ENSG00000223351
5	lnc-UBE2E2-2	chr3:22002908-22003032	ENSG00000223351

Variant related genes	Relation type
ZNF385D-AS2	TF binding region
ENSG00000110074	chromatin interactions

Extended variants
information (count: 1301 )
Associated
traits (count: 72 )

Variant overlapped rSNPs/rCNVs (count:1301 , 50 per page) page: 1 2 3 4 5 6 7 ... 27

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs9849994	chr3:21985380-21985381	Weak transcription Enhancers Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs542097835	chr3:21985402-21985403	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
3	rs529130011	chr3:21985407-21985408	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
4	rs519051	chr3:21985417-21985418	Enhancers Weak transcription Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
5	rs530936968	chr3:21985419-21985420	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
6	rs144381869	chr3:21985431-21985432	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
7	rs565925127	chr3:21985453-21985454	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
8	rs368012123	chr3:21985558-21985559	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
9	rs186236864	chr3:21985561-21985562	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
10	rs189870285	chr3:21985574-21985575	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
11	rs182069765	chr3:21985612-21985613	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
12	rs565986364	chr3:21985622-21985623	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
13	rs529994784	chr3:21985641-21985642	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
14	rs377088457	chr3:21985654-21985655	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
15	rs111567741	chr3:21985674-21985675	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
16	rs521724	chr3:21985691-21985692	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
17	rs148788193	chr3:21985701-21985702	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
18	rs558635467	chr3:21985764-21985765	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
19	rs34541965	chr3:21985765-21985766	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
20	rs522590	chr3:21985766-21985767	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
21	rs1684484	chr3:21985774-21985775	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
22	rs188274383	chr3:21985792-21985793	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
23	rs142468872	chr3:21985802-21985803	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
24	rs367606175	chr3:21985829-21985830	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
25	rs17582553	chr3:21985831-21985832	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
26	rs376806618	chr3:21985858-21985859	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
27	rs575810482	chr3:21985868-21985869	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
28	rs671377	chr3:21985871-21985872	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
29	rs564572080	chr3:21985885-21985886	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
30	rs192609058	chr3:21985887-21985888	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
31	rs141967828	chr3:21985890-21985891	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
32	rs183205082	chr3:21985891-21985892	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
33	rs555352742	chr3:21985895-21985896	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
34	rs529975005	chr3:21985898-21985899	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
35	rs144295831	chr3:21985922-21985923	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
36	rs9870712	chr3:21985925-21985926	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
37	rs147809634	chr3:21985926-21985927	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
38	rs551908341	chr3:21985928-21985929	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
39	rs570222826	chr3:21985929-21985930	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
40	rs534408749	chr3:21985939-21985940	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
41	rs35533533	chr3:21985946-21985947	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
42	rs552576779	chr3:21985958-21985959	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
43	rs375060348	chr3:21985968-21985969	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
44	rs568031817	chr3:21986008-21986009	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
45	rs188485764	chr3:21986055-21986056	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
46	rs562855720	chr3:21986071-21986072	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
47	rs192141055	chr3:21986104-21986105	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
48	rs575797877	chr3:21986113-21986114	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
49	rs185069058	chr3:21986118-21986119	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
50	rs140271927	chr3:21986137-21986138	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:72)

Disease	PMID	Source
Medulloblastoma	21979893	CNVD
Esophageal squamous carcinoma	18405350	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Breast cancer	17603634	CNVD
Neuroblastoma	17327916	CNVD
Glioblastoma multiforme	21080181	CNVD
Neuroblastoma	18923191	CNVD
Colorectal cancer	21297112	CNVD
Lynch syndrome	18415027	CNVD
Renal cell carcinoma	18592004	CNVD
Acute myeloid leukemia	20729466	CNVD
Urothelial carcinoma	18382360	CNVD
Melanoma	18172304	CNVD
Cervical cancer	21062161	CNVD
Hirschsprung''s Disease	21712996	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Insulin resistance	16721378	CNVD
Neuroblastoma	18664255	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Multiple myeloma	17077331	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Ewing''s sarcoma	21437220	CNVD
Neuroblastoma	21484798	CNVD
Non-small cell lung cancer	21044232	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Oral cancer	19627613	CNVD
Renal cell carcinoma	19461508	CNVD
Epithelial cancer	22065749	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Acute myeloid leukemia	16864856	CNVD
Liposarcoma	21253554	CNVD
Basal cell lymphoma	21115979	CNVD
Endometrial cancer	22040021	CNVD
Pancreatic endocrine tumor	20981439	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	17387387	CNVD
Oral cancer	21386901	CNVD
Cutaneous squamous cell carcinomas	19131950	CNVD
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Retinoblastoma	21504564	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
lymphocytic leukemia	21291569	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Renal cell carcinoma	21668985	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Lung cancer	20668451	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Intellectual disability	22102821	CNVD
Esophageal cancer	20955586	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Myelofibrosis	22110671	CNVD
Gastric adenocarcinoma	19115996	CNVD
Squamous cell cancer	20885788	CNVD
Esophageal squamous carcinoma	17470683	CNVD
Breast cancer	17133270	CNVD
Uveal melanoma	20484589	CNVD
Autism	22495311	CNVD
Cancer	20164919	CNVD
Melanoma	20688739	CNVD

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:21982000-21987200	Weak transcription	Fetal Lung	lung
2	chr3:21984200-21985400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:21984600-21985600	Weak transcription	NHDF-Ad	bronchial
4	chr3:21984600-21985800	Weak transcription	Fetal Heart	heart
5	chr3:21984600-21985800	Enhancers	Pancreatic Islets	Pancreatic Islet
6	chr3:21984600-21986000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr3:21984600-21996000	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr3:21984800-21988400	Weak transcription	NHLF	lung
9	chr3:21985200-21986000	Active TSS	Fetal Stomach	stomach
10	chr3:21985200-21987400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr3:21985400-21985600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr3:21985400-21985800	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr3:21985400-21986200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:21985600-21985800	Enhancers	NHDF-Ad	bronchial
15	chr3:21985600-21986000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr3:21985600-21986000	Active TSS	Stomach Smooth Muscle	stomach
17	chr3:21985600-21986400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr3:21985800-21986200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
19	chr3:21985800-21986200	Enhancers	Fetal Heart	heart
20	chr3:21985800-21986200	Flanking Active TSS	NHDF-Ad	bronchial
21	chr3:21985800-21986400	Enhancers	Fetal Kidney	kidney
22	chr3:21985800-21986800	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr3:21986000-21986200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr3:21986000-21986200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr3:21986000-21986200	Enhancers	NH-A	brain
26	chr3:21986000-21986600	Weak transcription	Fetal Stomach	stomach
27	chr3:21986200-21987200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr3:21986200-21987200	Weak transcription	NHDF-Ad	bronchial
29	chr3:21986400-21986800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr3:21986400-21986800	Weak transcription	Fetal Kidney	kidney
31	chr3:21986800-21987200	Enhancers	Pancreatic Islets	Pancreatic Islet
32	chr3:21986800-21987600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr3:21986800-21987600	Enhancers	Fetal Kidney	kidney
34	chr3:21987200-21987400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:21987200-21987400	Enhancers	Fetal Stomach	stomach
36	chr3:21987200-21987400	Enhancers	NHDF-Ad	bronchial
37	chr3:21987200-21987600	Enhancers	Fetal Lung	lung
38	chr3:21987400-21987600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:21987400-21993000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr3:21988400-21988600	Enhancers	NHLF	lung
41	chr3:21992800-21994000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr3:21993000-21993800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr3:21993200-21994000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr3:21994000-21994400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr3:21994400-21994800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr3:21995600-21995800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr3:21995800-21996800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr3:21995800-21997400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr3:21995800-21997800	Enhancers	Liver	Liver
50	chr3:21996000-21996400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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