Variant report

Variant	nsv461314
Chromosome Location	chr4:28830639-28863159
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	chr4:28851851-28851992	HepG2	liver:	n/a	chr4:28851864-28851875
2	CTCF	chr4:28841783-28841844	Spleen_OC	spleen:	n/a	n/a
3	CTCF	chr4:28859090-28859160	ProgFib	skin:	n/a	n/a
4	CTCF	chr4:28856539-28856579	GM20000	blood:	n/a	n/a
5	CTCF	chr4:28843880-28844030	MCF-7	breast:	n/a	n/a
6	E2F4	chr4:28838724-28838884	MCF10A-Er-Src	breast:	n/a	n/a
7	EP300	chr4:28846728-28847161	T-47D	breast:	n/a	n/a
8	EP300	chr4:28836317-28836334	K562	blood:	n/a	n/a
9	FOXA1	chr4:28846736-28847146	T-47D	breast:	n/a	chr4:28846906-28846921
10	FOXA1	chr4:28846811-28847138	T-47D	breast:	n/a	chr4:28846906-28846921
11	FOXA1	chr4:28843923-28844243	T-47D	breast:	n/a	n/a
12	FOXA1	chr4:28832791-28833018	T-47D	breast:	n/a	n/a
13	FOXA1	chr4:28843921-28844248	T-47D	breast:	n/a	n/a
14	GATA3	chr4:28843900-28844248	T-47D	breast:	n/a	chr4:28844118-28844129
15	GATA3	chr4:28832776-28833110	T-47D	breast:	n/a	n/a
16	GATA3	chr4:28843897-28844233	T-47D	breast:	n/a	chr4:28844118-28844129
17	GATA3	chr4:28832744-28833124	T-47D	breast:	n/a	n/a
18	GATA3	chr4:28846843-28847101	T-47D	breast:	n/a	n/a
19	JUND	chr4:28852834-28852835	H1-hESC	embryonic stem cell:	n/a	n/a
20	MAFF	chr4:28833532-28833800	HepG2	liver:	n/a	n/a
21	MAFF	chr4:28833533-28833710	K562	blood:	n/a	n/a
22	MAFK	chr4:28833524-28833864	HepG2	liver:	n/a	n/a
23	MAFK	chr4:28833577-28833836	H1-hESC	embryonic stem cell:	n/a	n/a
24	MAFK	chr4:28833520-28833851	IMR90	lung:	n/a	n/a
25	MAFK	chr4:28845108-28845297	HepG2	liver:	n/a	n/a
26	MAFK	chr4:28833525-28833838	HepG2	liver:	n/a	n/a
27	NFYA	chr4:28830400-28830662	K562	blood:	n/a	n/a
28	NFYB	chr4:28830218-28830714	K562	blood:	n/a	n/a
29	NFYB	chr4:28830219-28830705	GM12878	blood:	n/a	n/a
30	POLR2A	chr4:28842947-28843389	H1-neurons	neurons:	n/a	n/a
31	POLR2A	chr4:28841834-28841866	Gliobla	brain:	n/a	n/a
32	POLR2A	chr4:28842550-28842827	MCF10A-Er-Src	breast:	n/a	n/a
33	POLR2A	chr4:28861909-28862085	MCF10A-Er-Src	breast:	n/a	n/a
34	POLR2A	chr4:28848455-28848529	MCF10A-Er-Src	breast:	n/a	n/a
35	POLR2A	chr4:28842386-28842408	MCF10A-Er-Src	breast:	n/a	n/a
36	POLR2A	chr4:28834654-28834761	MCF10A-Er-Src	breast:	n/a	n/a
37	POLR2A	chr4:28835725-28836070	H1-neurons	neurons:	n/a	n/a
38	POLR2A	chr4:28840384-28840515	MCF10A-Er-Src	breast:	n/a	n/a
39	POLR2A	chr4:28830710-28830845	Gliobla	brain:	n/a	n/a
40	POLR2A	chr4:28835691-28836110	H1-neurons	neurons:	n/a	n/a
41	POLR2A	chr4:28846065-28846185	ProgFib	skin:	n/a	n/a
42	POLR2A	chr4:28838352-28838362	MCF10A-Er-Src	breast:	n/a	n/a
43	REST	chr4:28842498-28843301	H1-neurons	neurons:	n/a	n/a
44	SPI1	chr4:28851784-28852040	HL-60	blood:	n/a	chr4:28851877-28851890
45	SPI1	chr4:28855011-28855191	K562	blood:	n/a	n/a
46	STAT3	chr4:28834039-28834239	MCF10A-Er-Src	breast:	n/a	n/a
47	STAT3	chr4:28833257-28833381	MCF10A-Er-Src	breast:	n/a	n/a
48	STAT3	chr4:28834933-28835023	MCF10A-Er-Src	breast:	n/a	n/a
49	STAT3	chr4:28837491-28837691	MCF10A-Er-Src	breast:	n/a	n/a
50	STAT3	chr4:28841115-28841308	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:28823073..28825418-chr4:28842573..28844204,2	MCF-7	breast:

Variant related genes	Relation type
MESTP3	TF binding region

Extended variants
information (count: 198 )
Associated
traits (count: 58 )

Variant overlapped rSNPs/rCNVs (count:198 , 50 per page) page: 1 2 3 4

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs10025330	chr4:28830639-28830640	Inactive region	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs28680249	chr4:28830642-28830643	Inactive region	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
3	rs530338589	chr4:28830645-28830646	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
4	rs565608067	chr4:28830646-28830647	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
5	rs531098240	chr4:28830648-28830649	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
6	rs116080031	chr4:28830651-28830652	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
7	rs574606668	chr4:28830652-28830653	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
8	rs530271733	chr4:28830658-28830659	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
9	rs142594782	chr4:28830665-28830666	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
10	rs118094602	chr4:28830680-28830681	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
11	rs186754229	chr4:28830686-28830687	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
12	rs551739461	chr4:28830689-28830690	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
13	rs568801530	chr4:28830692-28830693	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
14	rs537773149	chr4:28830703-28830704	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
15	rs115184503	chr4:28830707-28830708	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
16	rs568172515	chr4:28830708-28830709	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
17	rs533983000	chr4:28830709-28830710	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
18	rs553552972	chr4:28830713-28830714	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
19	rs573355583	chr4:28830718-28830719	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
20	rs146589457	chr4:28830739-28830740	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
21	rs374006456	chr4:28830740-28830741	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
22	rs544045995	chr4:28830743-28830744	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
23	rs189535332	chr4:28830750-28830751	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
24	rs575544493	chr4:28830751-28830752	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
25	rs544584651	chr4:28830753-28830754	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
26	rs28703048	chr4:28830755-28830756	Inactive region	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
27	rs10027777	chr4:28830758-28830759	Inactive region	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
28	rs552788832	chr4:28830771-28830772	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
29	rs559849497	chr4:28830772-28830773	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
30	rs532092518	chr4:28830778-28830779	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
31	rs143621201	chr4:28830780-28830781	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
32	rs562348724	chr4:28830781-28830782	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
33	rs146791365	chr4:28830789-28830790	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
34	rs548230248	chr4:28830796-28830797	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
35	rs568343243	chr4:28830806-28830807	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
36	rs181032885	chr4:28830810-28830811	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
37	rs547600877	chr4:28830811-28830812	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
38	rs570630020	chr4:28830813-28830814	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
39	rs539135621	chr4:28830818-28830819	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
40	rs547639587	chr4:28830819-28830820	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
41	rs111356524	chr4:28830820-28830821	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
42	rs558966171	chr4:28830821-28830822	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
43	rs575588238	chr4:28830827-28830828	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
44	rs573352839	chr4:28833404-28833405	Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs16881078	chr4:28833426-28833427	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
46	rs11737716	chr4:28833522-28833523	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
47	rs557411687	chr4:28833542-28833543	Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs574111408	chr4:28833587-28833588	Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs17653494	chr4:28833600-28833601	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
50	rs2029668	chr4:28833637-28833638	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a

Variant related diseases (count:58)

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
Cancer	20164919	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD
Tetralogy of Fallot	22912587	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:28833400-28835000	Enhancers	Fetal Heart	heart
2	chr4:28833600-28833800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr4:28834200-28835000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr4:28838000-28838400	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr4:28842400-28843200	Enhancers	Pancreatic Islets	Pancreatic Islet
6	chr4:28843200-28843600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr4:28843600-28844000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr4:28843600-28844000	Enhancers	Pancreatic Islets	Pancreatic Islet
9	chr4:28849400-28849600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr4:28859000-28859200	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
11	chr4:28859000-28859200	ZNF genes & repeats	Pancreas	Pancrea

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