Variant report

Variant	nsv1009464
Chromosome Location	chr4:27943970-27992849
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	chr4:27987127-27987522	GM12878	blood:	n/a	n/a
2	BHLHE40	chr4:27987261-27987451	GM12878	blood:	n/a	n/a
3	CEBPB	chr4:27946115-27946278	HepG2	liver:	n/a	chr4:27946212-27946225 chr4:27946213-27946224 chr4:27946212-27946225
4	CEBPB	chr4:27975320-27976363	Hela-S3	cervix:	n/a	n/a
5	CEBPB	chr4:27949094-27949157	HepG2	liver:	n/a	n/a
6	CHD2	chr4:27987288-27987388	GM12878	blood:	n/a	n/a
7	CTCF	chr4:27974691-27974811	Medullo	brain:	n/a	n/a
8	CTCF	chr4:27974860-27975010	HRPEpiC	eye:	n/a	n/a
9	CTCF	chr4:27957292-27957362	GM10266	blood:	n/a	n/a
10	CTCF	chr4:27974720-27974870	WERI-Rb-1	eye:	n/a	n/a
11	CUX1	chr4:27987280-27987441	GM12878	blood:	n/a	n/a
12	E2F4	chr4:27985393-27985540	MCF10A-Er-Src	breast:	n/a	n/a
13	E2F4	chr4:27987191-27987359	MCF10A-Er-Src	breast:	n/a	n/a
14	EBF1	chr4:27950136-27950447	GM12878	blood:	n/a	chr4:27950254-27950265
15	EP300	chr4:27975383-27975755	Hela-S3	cervix:	n/a	n/a
16	EP300	chr4:27987184-27987531	GM12878	blood:	n/a	n/a
17	EP300	chr4:27987186-27987443	GM12878	blood:	n/a	n/a
18	FOS	chr4:27974646-27974659	MCF10A-Er-Src	breast:	n/a	n/a
19	FOS	chr4:27973464-27973667	MCF10A-Er-Src	breast:	n/a	n/a
20	FOS	chr4:27975430-27975699	MCF10A-Er-Src	breast:	n/a	n/a
21	FOS	chr4:27985733-27985967	MCF10A-Er-Src	breast:	n/a	chr4:27985879-27985886 chr4:27985879-27985888
22	FOS	chr4:27975456-27975660	MCF10A-Er-Src	breast:	n/a	n/a
23	FOS	chr4:27975375-27975708	MCF10A-Er-Src	breast:	n/a	chr4:27975421-27975429
24	FOS	chr4:27946200-27946239	MCF10A-Er-Src	breast:	n/a	n/a
25	FOS	chr4:27985868-27985905	MCF10A-Er-Src	breast:	n/a	chr4:27985879-27985886 chr4:27985879-27985888
26	FOS	chr4:27974646-27974744	MCF10A-Er-Src	breast:	n/a	n/a
27	FOS	chr4:27975360-27975595	MCF10A-Er-Src	breast:	n/a	chr4:27975421-27975429
28	FOS	chr4:27946070-27946268	MCF10A-Er-Src	breast:	n/a	n/a
29	FOS	chr4:27975358-27975690	Hela-S3	cervix:	n/a	chr4:27975421-27975429
30	FOSL2	chr4:27975300-27975748	MCF-7	breast:	n/a	chr4:27975421-27975429
31	GATA3	chr4:27975328-27975809	MCF-7	breast:	n/a	n/a
32	GATA3	chr4:27975170-27975976	MCF-7	breast:	n/a	n/a
33	GATA3	chr4:27975312-27975579	MCF-7	breast:	n/a	n/a
34	GATA3	chr4:27975415-27975654	MCF-7	breast:	n/a	n/a
35	JUN	chr4:27975357-27975770	Hela-S3	cervix:	n/a	chr4:27975421-27975429
36	JUN	chr4:27973455-27973575	HepG2	liver:	n/a	chr4:27973549-27973562
37	JUND	chr4:27973469-27973669	HepG2	liver:	n/a	n/a
38	JUND	chr4:27985771-27986007	HepG2	liver:	n/a	chr4:27985879-27985886 chr4:27985877-27985888 chr4:27985879-27985888
39	JUND	chr4:27975350-27976016	Hela-S3	cervix:	n/a	chr4:27975421-27975429
40	MAFF	chr4:27953673-27953942	HepG2	liver:	n/a	chr4:27953794-27953812 chr4:27953767-27953785
41	MAFF	chr4:27988246-27988546	HepG2	liver:	n/a	chr4:27988410-27988428
42	MAFK	chr4:27988291-27988514	HepG2	liver:	n/a	chr4:27988364-27988379
43	MAFK	chr4:27953625-27954004	HepG2	liver:	n/a	chr4:27953769-27953784 chr4:27953774-27953783
44	MAFK	chr4:27953708-27954004	IMR90	lung:	n/a	chr4:27953769-27953784 chr4:27953774-27953783
45	MAFK	chr4:27972574-27972702	HepG2	liver:	n/a	n/a
46	MAFK	chr4:27953732-27953918	HepG2	liver:	n/a	chr4:27953769-27953784 chr4:27953774-27953783
47	MAFK	chr4:27988253-27988583	HepG2	liver:	n/a	chr4:27988364-27988379
48	MAZ	chr4:27960567-27960689	HepG2	liver:	n/a	n/a
49	MXI1	chr4:27987392-27987401	GM12878	blood:	n/a	n/a
50	MYC	chr4:27975478-27975678	MCF10A-Er-Src	breast:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:27979369-27979419	Jurkat	blood:	n/a
2	chr4:27979369-27979419	SKMC	muscle:	n/a
3	chr4:27979369-27979419	HIPEpiC	eye:	n/a
4	chr4:27979369-27979419	SK-N-SH	brain:	n/a
5	chr4:27979369-27979419	GM19239	blood:	n/a
6	chr4:27979369-27979419	ProgFib	skin:	n/a
7	chr4:27979369-27979419	HAEpiC	amniotic membrane:	n/a
8	chr4:27979369-27979419	NH-A	brain:	n/a
9	chr4:27979369-27979419	MCF-7	breast:	n/a
10	chr4:27979369-27979419	HPAEpiC	pulmonary alveolar:	n/a
11	chr4:27979369-27979419	HCPEpiC	choroid plexus:	n/a
12	chr4:27979369-27979419	U87	brain:	n/a
13	chr4:27979369-27979419	NHDF-neo	bronchial:	n/a
14	chr4:27979369-27979419	MCF10A-Er-Src	breast:	n/a
15	chr4:27979369-27979419	HEK293	kidney:	embryo
16	chr4:27979369-27979419	SK-N-MC	brain:	n/a
17	chr4:27979369-27979419	BE2_C	brain:	n/a
18	chr4:27979369-27979419	IMR90	lung:	fetal
19	chr4:27979369-27979419	HCT-116	colon:	n/a
20	chr4:27979369-27979419	PANC-1	pancreas:	n/a
21	chr4:27979369-27979419	NHBE	bronchial:	n/a
22	chr4:27979369-27979419	T-47D	breast:	n/a
23	chr4:27979369-27979419	HCM	heart:	n/a
24	chr4:27979369-27979419	GM06990	blood:	n/a
25	chr4:27979369-27979419	HMEC	breast:	n/a
26	chr4:27979369-27979419	CMK	blood:	n/a
27	chr4:27979369-27979419	HNPCEpiC	eye:	n/a
28	chr4:27979369-27979419	NB4	blood:	n/a
29	chr4:27979369-27979419	Hepatocyte	liver:	n/a
30	chr4:27979369-27979419	GM12892	blood:	n/a
31	chr4:27979369-27979419	HL-60	blood:	n/a
32	chr4:27979369-27979419	AoSMC	blood vessel:	n/a
33	chr4:27979369-27979419	RPTEC	kidney:	n/a
34	chr4:27979369-27979419	LNCaP	prostate:	n/a
35	chr4:27979369-27979419	K562	blood:	n/a
36	chr4:27979369-27979419	HRPEpiC	eye:	n/a
37	chr4:27979369-27979419	ovcar-3	ovarian:	n/a
38	chr4:27979369-27979419	Hela-S3	cervix:	n/a
39	chr4:27979369-27979419	SK-N-SH_RA	brain:	n/a
40	chr4:27979369-27979419	BJ	skin:	n/a
41	chr4:27979369-27979419	HEEpiC	esophagus:	n/a
42	chr4:27979369-27979419	HRCEpiC	kidney:	n/a
43	chr4:27979369-27979419	PFSK-1	brain:	n/a
44	chr4:27979369-27979419	AG04449	skin:	fetal
45	chr4:27979369-27979419	HRE	kidney:	n/a
46	chr4:27979369-27979419	HUVEC	blood vessel:	n/a
47	chr4:27979369-27979419	A549	lung:	n/a
48	chr4:27979369-27979419	GM12891	blood:	n/a
49	chr4:27979369-27979419	HCF	heart:	n/a
50	chr4:27979369-27979419	AG09319	gingival:	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:27971353..27973637-chr4:27975179..27977202,2	MCF-7	breast:
2	chr4:27971353..27973637-chr4:27975179..27977202,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RP11-180C1.1.1-4	chr4:27973018-27973312	l_2620_chr4:27973017-27981533_testes
2	lnc-RP11-180C1.1.1-4	chr4:27981420-27981533	l_2620_chr4:27973017-27981533_testes
3	lnc-RP11-180C1.1.1-1	chr4:27969345-27969549	XLOC_003916
4	lnc-RP11-180C1.1.1-1	chr4:27986291-27986685	XLOC_003916

Variant related genes	Relation type
ENSG00000251410	TF binding region
ENSG00000251410	CpG island

Extended variants
information (count: 818 )
Associated
traits (count: 54 )

Variant overlapped rSNPs/rCNVs (count:818 , 50 per page) page: 1 2 3 4 5 6 7 ... 17

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs529947477	chr4:27947023-27947024	Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs12644890	chr4:27947063-27947064	Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs565774669	chr4:27947081-27947082	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs534679821	chr4:27947124-27947125	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs551485813	chr4:27947206-27947207	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs571674638	chr4:27947207-27947208	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs141273077	chr4:27947222-27947223	Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs557284209	chr4:27947240-27947241	Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs540297853	chr4:27947245-27947246	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs28499183	chr4:27947246-27947247	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs182454479	chr4:27947252-27947253	Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs553694943	chr4:27947262-27947263	Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs572911559	chr4:27947276-27947277	Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs544998960	chr4:27947283-27947284	Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs189112172	chr4:27947352-27947353	Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs575253461	chr4:27947361-27947362	Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs146956703	chr4:27947389-27947390	Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs34237856	chr4:27947420-27947421	Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs11324622	chr4:27947421-27947422	Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs397992729	chr4:27947430-27947431	Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs193133744	chr4:27947463-27947464	Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs529887567	chr4:27947584-27947585	Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs546521331	chr4:27947617-27947618	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs559990212	chr4:27947663-27947664	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs560035026	chr4:27947681-27947682	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs529074403	chr4:27947684-27947685	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs532243215	chr4:27947753-27947754	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs185593182	chr4:27947775-27947776	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs571579781	chr4:27947776-27947777	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs184009522	chr4:27947781-27947782	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs537154058	chr4:27947794-27947795	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs551052506	chr4:27947832-27947833	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs9990661	chr4:27947900-27947901	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
34	rs9990917	chr4:27947953-27947954	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
35	rs374048462	chr4:27947957-27947958	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs188554360	chr4:27947968-27947969	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs539298564	chr4:27947975-27947976	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs558271294	chr4:27947983-27947984	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs575173269	chr4:27947994-27947995	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs147981954	chr4:27948002-27948003	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs554632014	chr4:27948004-27948005	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs2192542	chr4:27948005-27948006	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
43	rs192110502	chr4:27948008-27948009	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs184199112	chr4:27948037-27948038	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs551714461	chr4:27948057-27948058	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs559884240	chr4:27948065-27948066	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs532286123	chr4:27948097-27948098	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs546034453	chr4:27948098-27948099	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs77967861	chr4:27948136-27948137	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs530926341	chr4:27948158-27948159	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:54)

Disease	PMID	Source
Chronic lymphocytic leukemia	21546498	CNVD
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Colorectal cancer	19359472	CNVD
Neuroblastoma	17533364	CNVD
Oral squamous cell carcinoma	17134496	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
T-cell prolymphocytic leukemia	19278963	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Breast cancer	21785460	CNVD
Chronic lymphocytic leukemia	20421269	CNVD
Lung cancer	18438408	CNVD
Wilms tumour	21544195	CNVD
Breast cancer	21858162	CNVD
small cell lung cancer	20016488	CNVD
Cancer	21183584	CNVD
Small bowel adenocarcinoma	21586687	CNVD
Gastric cancer	21586687	CNVD
lymphocytic leukemia	21291569	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	16608533	CNVD
Non-small cell lung cancer	21829676	CNVD
Melanoma	22183965	CNVD
Multiple myeloma	17550852	CNVD
Prostate cancer	18632612	CNVD
Olfactory neuroblastoma	18408657	CNVD
Burkitt''s lymphoma	20823134	CNVD
Cancer	22183965	CNVD
Melanoma	18172304	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Prostate cancer	16573809	CNVD
Myelofibrosis	22110671	CNVD

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:27947000-27947600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr4:27947600-27949200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr4:27949200-27949400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr4:27970600-27971600	Enhancers	iPS-20b Cell Line	embryonic stem cell
5	chr4:27971000-27971600	Enhancers	H1 Cell Line	embryonic stem cell
6	chr4:27971200-27971600	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr4:27975000-27975600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr4:27975000-27976600	Enhancers	Hela-S3	cervix
9	chr4:27975600-27976800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr4:27975800-27976400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr4:27976800-27979400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr4:27979400-27980400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr4:27980400-27981400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr4:27981400-27982600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr4:27984000-27984200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr4:27984400-27985200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr4:27985200-27989000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr4:27986200-27986600	Enhancers	Brain Anterior Caudate	brain
19	chr4:27986600-27987000	Enhancers	Fetal Brain Female	brain
20	chr4:27986600-27988000	Weak transcription	Brain Anterior Caudate	brain
21	chr4:27987800-27988400	Enhancers	Fetal Heart	heart
22	chr4:27988000-27988200	Enhancers	Brain Anterior Caudate	brain
23	chr4:27989000-27989200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr4:27991600-27992200	Active TSS	Brain Hippocampus Middle	brain

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