Variant report

Variant	nsv961778
Chromosome Location	chr2:55659501-55668562
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	ARID3A	chr2:55659185-55659546	K562	blood:	n/a	n/a
2	CBX3	chr2:55659045-55659624	HCT-116	colon:	n/a	n/a
3	CBX3	chr2:55665756-55666104	K562	blood:	n/a	n/a
4	CEBPB	chr2:55660639-55660797	HepG2	liver:	n/a	n/a
5	CEBPB	chr2:55666260-55666481	HepG2	liver:	n/a	chr2:55666327-55666338
6	CEBPB	chr2:55660788-55660798	A549	lung:	n/a	n/a
7	CEBPB	chr2:55660671-55660809	K562	blood:	n/a	n/a
8	CREB1	chr2:55668553-55669043	K562	blood:	n/a	n/a
9	CTCF	chr2:55659126-55659507	A549	lung:	n/a	chr2:55659337-55659355 chr2:55659332-55659353 chr2:55659338-55659354
10	CTCF	chr2:55659603-55659625	GM10248	blood:	n/a	n/a
11	CTCF	chr2:55661723-55661750	GM13976	blood:	n/a	n/a
12	CTCF	chr2:55661140-55661290	GM12874	blood:	n/a	n/a
13	CTCF	chr2:55659160-55659521	H1-hESC	embryonic stem cell:	n/a	chr2:55659337-55659355 chr2:55659332-55659353 chr2:55659338-55659354
14	CTCF	chr2:55659440-55659590	GM12864	blood:	n/a	n/a
15	CTCF	chr2:55659152-55659516	K562	blood:	n/a	chr2:55659337-55659355 chr2:55659332-55659353 chr2:55659338-55659354
16	CTCF	chr2:55659096-55659575	HCT-116	colon:	n/a	chr2:55659337-55659355 chr2:55659332-55659353 chr2:55659338-55659354
17	CTCF	chr2:55659161-55659556	HepG2	liver:	n/a	chr2:55659337-55659355 chr2:55659332-55659353 chr2:55659338-55659354
18	CTCF	chr2:55659580-55659730	AG10803	skin:	n/a	n/a
19	CTCF	chr2:55660040-55660190	AG10803	skin:	n/a	n/a
20	CTCF	chr2:55659420-55659570	NHEK	skin:	n/a	n/a
21	CTCF	chr2:55659058-55659636	HCT-116	colon:	n/a	chr2:55659337-55659355 chr2:55659332-55659353 chr2:55659338-55659354
22	CTCF	chr2:55659036-55659705	SK-N-SH	brain:	n/a	chr2:55659337-55659355 chr2:55659332-55659353 chr2:55659338-55659354
23	CTCF	chr2:55659580-55659730	AG09319	gingival:	n/a	n/a
24	CTCF	chr2:55659106-55659584	MCF-7	breast:	n/a	chr2:55659337-55659355 chr2:55659332-55659353 chr2:55659338-55659354
25	CTCF	chr2:55659160-55659529	IMR90	lung:	n/a	chr2:55659337-55659355 chr2:55659332-55659353 chr2:55659338-55659354
26	CTCF	chr2:55664920-55665070	HepG2	liver:	n/a	n/a
27	CTCF	chr2:55659135-55659541	GM12878	blood:	n/a	chr2:55659337-55659355 chr2:55659332-55659353 chr2:55659338-55659354
28	CTCF	chr2:55659075-55659620	K562	blood:	n/a	chr2:55659337-55659355 chr2:55659332-55659353 chr2:55659338-55659354
29	CTCF	chr2:55659209-55659501	A549	lung:	n/a	chr2:55659337-55659355 chr2:55659332-55659353 chr2:55659338-55659354
30	CTCF	chr2:55658237-55659876	A549	lung:	n/a	chr2:55659337-55659355 chr2:55659332-55659353 chr2:55659338-55659354
31	GATA1	chr2:55668290-55669044	K562	blood:	n/a	chr2:55668531-55668541 chr2:55668533-55668540 chr2:55668533-55668540 chr2:55668533-55668540
32	JUN	chr2:55659172-55659514	K562	blood:	n/a	n/a
33	JUND	chr2:55668442-55669013	K562	blood:	n/a	n/a
34	MAX	chr2:55665914-55665920	HepG2	liver:	n/a	n/a
35	POLR2A	chr2:55665807-55665907	HepG2	liver:	n/a	n/a
36	POLR2A	chr2:55665418-55665425	MCF-7	breast:	n/a	n/a
37	RAD21	chr2:55659219-55659512	H1-hESC	embryonic stem cell:	n/a	n/a
38	RAD21	chr2:55658967-55659602	A549	lung:	n/a	n/a
39	RAD21	chr2:55659111-55659509	H1-hESC	embryonic stem cell:	n/a	n/a
40	RAD21	chr2:55659079-55659641	A549	lung:	n/a	n/a
41	RAD21	chr2:55659103-55659528	SK-N-SH_RA	brain:	n/a	n/a
42	RAD21	chr2:55659116-55659530	GM12878	blood:	n/a	n/a
43	RAD21	chr2:55659071-55659554	ECC-1	luminal epithelium:	n/a	n/a
44	RAD21	chr2:55659051-55659575	ECC-1	luminal epithelium:	n/a	n/a
45	RAD21	chr2:55659027-55659616	HepG2	liver:	n/a	n/a
46	RAD21	chr2:55659135-55659532	IMR90	lung:	n/a	n/a
47	RAD21	chr2:55658663-55659797	SK-N-SH	brain:	n/a	n/a
48	RAD21	chr2:55659189-55659622	MCF-7	breast:	n/a	n/a
49	RAD21	chr2:55659007-55659568	HCT-116	colon:	n/a	n/a
50	RAD21	chr2:55658951-55659570	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:55458753..55460899-chr2:55659427..55661705,2	MCF-7	breast:
2	chr2:55645665..55649753-chr2:55657366..55660139,6	K562	blood:
3	chr2:55653744..55655531-chr2:55659781..55661813,3	K562	blood:
4	chr2:55652880..55655236-chr2:55657266..55660173,3	MCF-7	breast:
5	chr2:55659643..55661172-chr2:55741607..55744341,2	MCF-7	breast:
6	chr2:55462241..55464416-chr2:55656583..55659722,3	MCF-7	breast:
7	chr2:55463171..55466180-chr2:55659869..55661423,3	MCF-7	breast:
8	chr2:55652771..55655244-chr2:55659480..55661281,2	K562	blood:
9	chr2:55647253..55647758-chr2:55659096..55659834,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CCDC88A-1	chr2:55662292-55662758	NONHSAT070788

Variant related genes	Relation type
BTF3P5	TF binding region
ENSG00000143947	chromatin interactions
ENSG00000162994	chromatin interactions
ENSG00000115355	chromatin interactions

Extended variants
information (count: 251 )
Associated
traits (count: 80 )

Variant overlapped rSNPs/rCNVs (count:251 , 50 per page) page: 1 2 3 4 5 6

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs13415672	chr2:55659501-55659502	Enhancers Weak transcription	Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs146837986	chr2:55659634-55659635	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
3	rs140910354	chr2:55659707-55659708	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
4	rs115156706	chr2:55659736-55659737	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
5	rs186652964	chr2:55659746-55659747	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
6	rs528452973	chr2:55659793-55659794	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
7	rs35846240	chr2:55659797-55659798	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
8	rs374929170	chr2:55659809-55659810	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
9	rs556996459	chr2:55659817-55659818	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
10	rs201481125	chr2:55659852-55659853	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
11	rs563129211	chr2:55659867-55659868	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
12	rs375072892	chr2:55659869-55659870	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
13	rs190237550	chr2:55659870-55659871	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
14	rs557083044	chr2:55659921-55659922	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
15	rs13029621	chr2:55659970-55659971	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
16	rs540088815	chr2:55659978-55659979	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
17	rs182574655	chr2:55659980-55659981	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
18	rs572826679	chr2:55660000-55660001	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
19	rs144638134	chr2:55660050-55660051	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
20	rs555544765	chr2:55660068-55660069	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
21	rs76268639	chr2:55660069-55660070	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
22	rs76373346	chr2:55660129-55660130	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
23	rs564233497	chr2:55660158-55660159	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
24	rs533093092	chr2:55660166-55660167	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
25	rs528205553	chr2:55660212-55660213	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
26	rs72915986	chr2:55660220-55660221	Weak transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
27	rs185348952	chr2:55660228-55660229	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
28	rs189712662	chr2:55660287-55660288	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
29	rs568215139	chr2:55660348-55660349	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
30	rs182375333	chr2:55660349-55660350	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
31	rs35883596	chr2:55660372-55660373	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
32	rs372786455	chr2:55660387-55660388	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
33	rs138585086	chr2:55660394-55660395	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
34	rs539625941	chr2:55660438-55660439	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
35	rs569528590	chr2:55660465-55660466	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
36	rs140260645	chr2:55660495-55660496	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
37	rs10187983	chr2:55660508-55660509	Weak transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
38	rs189229158	chr2:55660590-55660591	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
39	rs558300884	chr2:55660633-55660634	Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
40	rs571726024	chr2:55660653-55660654	Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
41	rs12471421	chr2:55660659-55660660	Enhancers	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
42	rs369275103	chr2:55660678-55660679	Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
43	rs370022907	chr2:55660682-55660683	Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
44	rs575423191	chr2:55660711-55660712	Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
45	rs552782616	chr2:55660721-55660722	Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
46	rs552299474	chr2:55660792-55660793	Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
47	rs571061901	chr2:55660807-55660808	Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
48	rs193096652	chr2:55660811-55660812	Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
49	rs539795610	chr2:55660821-55660822	Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
50	rs557690749	chr2:55660861-55660862	Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:80)

Disease	PMID	Source
Medulloblastoma	21979893	CNVD
Lynch syndrome	18415027	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Ovarian neoplasms	16753589	CNVD
Glioblastoma multiforme	17387387	CNVD
Neuroblastoma	17533364	CNVD
Neuroblastoma	18923191	CNVD
Endometrial cancer	22040021	CNVD
Adrenal tumor	17535989	CNVD
Breast cancer	21264507	CNVD
Basal cell lymphoma	17053054	CNVD
Medulloblastoma	17522785	CNVD
Cancer	23418310	CNVD
Breast cancer	17603634	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Ependymoma	16718352	CNVD
lymphocytic leukemia	21291569	CNVD
Prostate cancer	18632612	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Intellectual disability	22102821	CNVD
Cancer	20164919	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Follicular lymphoma	20505157	CNVD
Autism	17483303	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Esophageal adenocarcinoma	18519675	CNVD
Medulloblastoma	20607354	CNVD
Leukemia	18628472	CNVD
Autism	22495311	CNVD
Autism	18522746	CNVD
Breast cancer	21785460	CNVD
Lung cancer	18438408	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Neuroblastoma	21508638	CNVD
Neurodevelopmental disorder	22521361	CNVD
Melanoma	18172304	CNVD
Cancer	16751803	CNVD
Colorectal cancer	16272173	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Williams Syndrome	20824207	CNVD
Breast cancer	16272173	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Ovarian cancer	21720365	CNVD
abnormal development	18461090	CNVD
Retinoblastoma	22278416	CNVD
Cancer	21183584	CNVD
Breast cancer	16397240	CNVD
Chronic lymphocytic leukemia	17053054	CNVD
Hereditary non-polyposis colorectal cancer	19566914	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
small cell lung cancer	20016488	CNVD
Developmental delay	21147756	CNVD
Mental retardation	19951919	CNVD
Myelofibrosis	22110671	CNVD
Microcephaly	20799320	CNVD
camptodactyly	20799320	CNVD
cognitive delay	20799320	CNVD
prenatal and postnatal growth deficiency	20799320	CNVD
ptosis of eyelids	20799320	CNVD
Maculopathy	20981449	CNVD
2p16.1 microdeletion syndrome	22283845	CNVD
Autism	22579565	CNVD
Autism	16963482	CNVD
Autism	21750575	CNVD
idiopathic intellectual disability	16963482	CNVD
Carcinoma ex pleomorphic adenoma	18828159	CNVD
Multiple myeloma	16616336	CNVD
Follicular lymphoma	17699855	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Ependymoma	20639864	CNVD
Melanoma	20877625	CNVD
Breast cancer	22522925	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55658400-55660600	Weak transcription	HepG2	liver
2	chr2:55659000-55659600	Enhancers	Liver	Liver
3	chr2:55660600-55661400	Enhancers	HepG2	liver
4	chr2:55664000-55664200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr2:55664800-55665200	Bivalent/Poised TSS	HepG2	liver
6	chr2:55665200-55665800	Flanking Bivalent TSS/Enh	HepG2	liver
7	chr2:55665800-55666000	Bivalent/Poised TSS	HepG2	liver
8	chr2:55666000-55666200	Active TSS	HepG2	liver
9	chr2:55666200-55666600	Enhancers	HepG2	liver
10	chr2:55668400-55668600	Enhancers	A549	lung
11	chr2:55668400-55669400	Enhancers	K562	blood

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