Variant report

Variant	nsv10240
Chromosome Location	chr3:611921-663701
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	chr3:638972-639242	GM12878	blood:	n/a	chr3:639093-639102
2	BRCA1	chr3:649451-649478	Hela-S3	cervix:	n/a	n/a
3	BRCA1	chr3:639591-639851	Hela-S3	cervix:	n/a	n/a
4	BRCA1	chr3:638578-639330	Hela-S3	cervix:	n/a	n/a
5	CEBPB	chr3:649124-649464	Hela-S3	cervix:	n/a	n/a
6	CEBPB	chr3:650039-650244	HepG2	liver:	n/a	chr3:650073-650084 chr3:650075-650084
7	CEBPB	chr3:638934-639824	Hela-S3	cervix:	n/a	n/a
8	CEBPB	chr3:650024-650224	A549	lung:	n/a	chr3:650073-650084 chr3:650075-650084
9	CEBPB	chr3:649955-650248	IMR90	lung:	n/a	chr3:650073-650084 chr3:650075-650084
10	CEBPB	chr3:637765-638119	Hela-S3	cervix:	n/a	n/a
11	CHD1	chr3:660628-660658	H1-hESC	embryonic stem cell:	n/a	n/a
12	CHD2	chr3:639101-639345	Hela-S3	cervix:	n/a	n/a
13	CTCF	chr3:616940-617090	HepG2	liver:	n/a	n/a
14	CTCF	chr3:659480-659630	GM12875	blood:	n/a	n/a
15	CTCF	chr3:658486-658533	A549	lung:	n/a	n/a
16	CTCF	chr3:641109-641158	ProgFib	skin:	n/a	n/a
17	CTCF	chr3:623741-623815	MCF-7	breast:	n/a	n/a
18	CTCF	chr3:655980-656130	GM12875	blood:	n/a	n/a
19	CTCF	chr3:616960-617110	Hela-S3	cervix:	n/a	n/a
20	CTCF	chr3:618424-618441	LNCaP	prostate:	n/a	n/a
21	CTCF	chr3:616980-617130	HEK293	kidney:	n/a	n/a
22	CTCF	chr3:617062-617147	MCF-7	breast:	n/a	n/a
23	CTCF	chr3:616940-617090	A549	lung:	n/a	n/a
24	CTCF	chr3:612832-612875	ProgFib	skin:	n/a	n/a
25	CTCF	chr3:650545-650626	ProgFib	skin:	n/a	n/a
26	CTCF	chr3:662427-662492	GM20000	blood:	n/a	n/a
27	CTCF	chr3:616998-617162	Hela-S3	cervix:	n/a	n/a
28	CTCF	chr3:615631-615719	ProgFib	skin:	n/a	n/a
29	CTCF	chr3:616960-617110	GM12870	blood:	n/a	n/a
30	CTCF	chr3:616960-617110	WERI-Rb-1	eye:	n/a	n/a
31	CTCF	chr3:616960-617110	GM12865	blood:	n/a	n/a
32	CTCF	chr3:616960-617110	SK-N-SH_RA	brain:	n/a	n/a
33	CTCF	chr3:612787-612876	GM13976	blood:	n/a	n/a
34	CTCF	chr3:623765-623780	ProgFib	skin:	n/a	n/a
35	CTCF	chr3:658448-658477	ProgFib	skin:	n/a	n/a
36	CTCF	chr3:617015-617090	LNCaP	prostate:	n/a	n/a
37	CTCF	chr3:616980-617130	HEEpiC	esophagus:	n/a	n/a
38	CTCF	chr3:626000-626150	NHDF-neo	bronchial:	n/a	n/a
39	CTCF	chr3:616980-617130	Caco-2	colon:	n/a	n/a
40	ELK1	chr3:639661-639775	Hela-S3	cervix:	n/a	n/a
41	ELK1	chr3:639134-639183	Hela-S3	cervix:	n/a	n/a
42	EP300	chr3:620995-621568	SK-N-SH	brain:	n/a	n/a
43	EP300	chr3:638941-639877	Hela-S3	cervix:	n/a	chr3:639272-639286
44	FOS	chr3:614457-614821	HUVEC	blood vessel:	n/a	n/a
45	FOXA2	chr3:623512-623895	A549	lung:	n/a	n/a
46	GABPA	chr3:638980-639383	Hela-S3	cervix:	n/a	n/a
47	GATA2	chr3:621236-621544	SH-SY5Y	brain:	n/a	chr3:621342-621349 chr3:621342-621353 chr3:621342-621349 chr3:621335-621356 chr3:621337-621353 chr3:621342-621349
48	GATA3	chr3:630942-631047	SH-SY5Y	brain:	n/a	n/a
49	GATA3	chr3:620053-620583	SH-SY5Y	brain:	n/a	chr3:620504-620525
50	GATA3	chr3:636965-637085	SH-SY5Y	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr21:9533639..9536328-chr3:614645..617390,2	MCF-7	breast:
2	chr21:9517250..9519290-chr3:632442..635070,2	MCF-7	breast:
3	chr21:9537493..9539688-chr3:612236..614804,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-IL5RA-14	chr3:659472-659997	NONHSAT087571
2	lnc-CHL1-3	chr3:633788-633866	ENSG00000224957
3	lnc-CHL1-3	chr3:633788-633866	NR_110118

Variant related genes	Relation type
ENSG00000238075	TF binding region
DCBLD2	miRNA target sites

Extended variants
information (count: 573 )
Associated
traits (count: 82 )

Variant overlapped rSNPs/rCNVs (count:573 , 50 per page) page: 1 2 3 4 5 6 7 ... 12

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs545695081	chr3:611985-611986	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs560503947	chr3:612010-612011	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs116245793	chr3:612031-612032	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs9862617	chr3:612055-612056	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
5	rs548117325	chr3:612082-612083	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs184722949	chr3:612099-612100	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs531546006	chr3:612110-612111	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs75462368	chr3:612152-612153	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs578199213	chr3:612176-612177	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs189439134	chr3:612181-612182	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs547274861	chr3:612184-612185	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs539546283	chr3:612203-612204	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs9867540	chr3:612215-612216	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
14	rs111363618	chr3:612222-612223	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs142907564	chr3:612267-612268	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs4684486	chr3:612268-612269	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs7645799	chr3:612269-612270	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs2729148	chr3:612273-612274	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
19	rs556506772	chr3:612283-612284	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs533831281	chr3:612285-612286	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs112207968	chr3:612287-612288	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs35127358	chr3:612291-612292	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs558683518	chr3:612292-612293	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs545728122	chr3:612318-612319	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs560737611	chr3:612347-612348	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs79149229	chr3:612348-612349	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs151066934	chr3:612361-612362	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs80095906	chr3:612368-612369	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs35322394	chr3:612374-612375	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
30	rs561327011	chr3:612380-612381	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs2930517	chr3:612388-612389	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs531761900	chr3:612396-612397	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs550229814	chr3:612399-612400	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs189227490	chr3:612614-612615	Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs57220106	chr3:612620-612621	Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs571887890	chr3:612632-612633	Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs539186718	chr3:612642-612643	Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs181023038	chr3:612649-612650	Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs2955649	chr3:612677-612678	Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs2930515	chr3:612683-612684	Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs572819462	chr3:612714-612715	Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs543304068	chr3:612750-612751	Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs554696147	chr3:612772-612773	Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs576371857	chr3:612773-612774	Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs186842091	chr3:612793-612794	Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs2729211	chr3:633816-633817	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
47	rs559342256	chr3:633819-633820	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
48	rs146518297	chr3:633829-633830	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
49	rs5846012	chr3:633849-633850	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
50	rs145631971	chr3:636403-636404	Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:82)

Disease	PMID	Source
Cancer	20164920	CNVD
Lung cancer	16618734	CNVD
Autism	18349135	CNVD
Breast cancer	20409316	CNVD
Myelofibrosis	22110671	CNVD
Autism	22241247	CNVD
Intellectual disability	22045946	CNVD
Squamous cell cancer	19607727	CNVD
Gastric adenocarcinoma	19115996	CNVD
sporadic birth defects	19047251	CNVD
Mental retardation	17124404	CNVD
abnormal development	18461090	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Sudden cardiac death	19188705	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Ovarian cancer	21720365	CNVD
Neuroblastoma	18923191	CNVD
Papillary thyroid carcinoma	21436994	CNVD
Biliary cancer	19435499	CNVD
Medulloblastoma	21979893	CNVD
Esophageal squamous carcinoma	18405350	CNVD
Breast cancer	17603634	CNVD
Neuroblastoma	17327916	CNVD
Glioblastoma multiforme	21080181	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
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
small cell lung cancer	20016488	CNVD
Breast cancer	21364760	CNVD
Schizophrenia	20967226	CNVD
Autism	22543975	CNVD
Attention deficit hyperactivity disorder	19546859	CNVD
lymphocytic leukemia	21291569	CNVD
Non-syndromic sensorineural hearing loss	17289997	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Renal cell carcinoma	21668985	CNVD
Tetralogy of Fallot	22912587	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Autism	20685689	CNVD
Multiple myeloma	17550852	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Hodgkin''s lymphoma	17606441	CNVD
early-passage human iPS cells	21368824	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:611200-612400	Weak transcription	Fetal Brain Male	brain
2	chr3:612600-612800	Enhancers	Fetal Brain Male	brain
3	chr3:636400-642600	Enhancers	Hela-S3	cervix
4	chr3:639200-639800	Enhancers	Dnd41	blood
5	chr3:649000-650000	Enhancers	Hela-S3	cervix
6	chr3:649200-650200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr3:659600-660000	Active TSS	Spleen	Spleen
8	chr3:663600-664000	Enhancers	Fetal Brain Male	brain

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