Variant report

Variant	nsv533650
Chromosome Location	chr2:52844384-52885500
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	CTCF	chr2:52859831-52859939	Gliobla	brain:	n/a	chr2:52859875-52859891 chr2:52859876-52859889
2	CTCF	chr2:52879995-52880027	Spleen_OC	spleen:	n/a	n/a
3	CTCF	chr2:52859760-52859910	HBMEC	blood vessel:	n/a	chr2:52859875-52859891 chr2:52859876-52859889
4	CTCF	chr2:52859800-52859950	HCT-116	colon:	n/a	chr2:52859875-52859891 chr2:52859876-52859889
5	CTCF	chr2:52859851-52859922	MCF-7	breast:	n/a	chr2:52859875-52859891 chr2:52859876-52859889
6	CTCF	chr2:52859846-52859923	MCF-7	breast:	n/a	chr2:52859875-52859891 chr2:52859876-52859889
7	CTCF	chr2:52859840-52859990	A549	lung:	n/a	chr2:52859875-52859891 chr2:52859876-52859889
8	CTCF	chr2:52859869-52859905	MCF-7	breast:	n/a	chr2:52859875-52859891 chr2:52859876-52859889
9	CTCF	chr2:52859794-52859958	H1-hESC	embryonic stem cell:	n/a	chr2:52859875-52859891 chr2:52859876-52859889
10	CTCF	chr2:52859678-52859968	H1-hESC	embryonic stem cell:	n/a	chr2:52859875-52859891 chr2:52859876-52859889
11	CTCF	chr2:52882089-52882193	Lung_OC	lung:	n/a	n/a
12	CTCF	chr2:52880496-52880544	GM20000	blood:	n/a	n/a
13	CTCF	chr2:52859820-52859970	BE2_C	brain:	n/a	chr2:52859875-52859891 chr2:52859876-52859889
14	CTCF	chr2:52859820-52859942	MCF-7	breast:	n/a	chr2:52859875-52859891 chr2:52859876-52859889
15	CTCF	chr2:52859780-52860019	H1-hESC	embryonic stem cell:	n/a	chr2:52859875-52859891 chr2:52859876-52859889
16	CTCF	chr2:52862960-52863110	GM12868	blood:	n/a	n/a
17	CTCF	chr2:52859850-52859915	Hela-S3	cervix:	n/a	chr2:52859875-52859891 chr2:52859876-52859889
18	CTCF	chr2:52859780-52859930	WERI-Rb-1	eye:	n/a	chr2:52859875-52859891 chr2:52859876-52859889
19	CTCF	chr2:52859820-52859970	HCT-116	colon:	n/a	chr2:52859875-52859891 chr2:52859876-52859889
20	CTCF	chr2:52859846-52859932	A549	lung:	n/a	chr2:52859875-52859891 chr2:52859876-52859889
21	CTCF	chr2:52882954-52883036	GM13976	blood:	n/a	n/a
22	E2F4	chr2:52864218-52864453	MCF10A-Er-Src	breast:	n/a	n/a
23	FOS	chr2:52871879-52872072	MCF10A-Er-Src	breast:	n/a	n/a
24	JUND	chr2:52845306-52845506	H1-hESC	embryonic stem cell:	n/a	chr2:52845322-52845334
25	KAP1	chr2:52875145-52875554	K562	blood:	n/a	n/a
26	MAZ	chr2:52884974-52885174	HepG2	liver:	n/a	n/a
27	MYC	chr2:52851072-52851240	MCF10A-Er-Src	breast:	n/a	n/a
28	POLR2A	chr2:52872147-52872231	MCF10A-Er-Src	breast:	n/a	n/a
29	POLR2A	chr2:52864094-52864150	MCF10A-Er-Src	breast:	n/a	n/a
30	POLR2A	chr2:52866350-52866369	MCF10A-Er-Src	breast:	n/a	n/a
31	POLR2A	chr2:52851149-52851173	MCF10A-Er-Src	breast:	n/a	n/a
32	POLR2A	chr2:52858934-52859019	A549	lung:	n/a	n/a
33	POLR2A	chr2:52871660-52871855	GM12878	blood:	n/a	n/a
34	POLR2A	chr2:52875078-52875223	A549	lung:	n/a	n/a
35	POLR2A	chr2:52858854-52858890	ProgFib	skin:	n/a	n/a
36	POLR2A	chr2:52883965-52884045	A549	lung:	n/a	n/a
37	POLR2A	chr2:52865707-52865808	GM12878	blood:	n/a	n/a
38	RAD21	chr2:52859679-52860093	H1-hESC	embryonic stem cell:	n/a	n/a
39	RAD21	chr2:52859633-52860028	H1-hESC	embryonic stem cell:	n/a	n/a
40	RAD21	chr2:52859681-52860066	H1-hESC	embryonic stem cell:	n/a	n/a
41	REST	chr2:52863930-52864236	HL-60	blood:	n/a	n/a
42	REST	chr2:52863955-52864161	Hela-S3	cervix:	n/a	n/a
43	REST	chr2:52863907-52864116	H1-hESC	embryonic stem cell:	n/a	n/a
44	REST	chr2:52863929-52864260	ECC-1	luminal epithelium:	n/a	n/a
45	REST	chr2:52863940-52864143	Hela-S3	cervix:	n/a	n/a
46	SETDB1	chr2:52875139-52875470	U2OS	brain:	n/a	n/a
47	SPI1	chr2:52854802-52855055	GM12878	blood:	n/a	n/a
48	SPI1	chr2:52849087-52849403	HL-60	blood:	n/a	chr2:52849208-52849221 chr2:52849374-52849387
49	STAT3	chr2:52864136-52864294	MCF10A-Er-Src	breast:	n/a	n/a
50	STAT3	chr2:52854730-52854742	MCF10A-Er-Src	breast:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:52860117-52860167	BE2_C	brain:	n/a
2	chr2:52860117-52860167	BE2_C	brain:	n/a
3	chr2:52856751-52856801	HMEC	breast:	n/a
4	chr2:52856918-52856968	BJ	skin:	n/a
5	chr2:52856751-52856801	HRE	kidney:	n/a
6	chr2:52856751-52856801	NH-A	brain:	n/a
7	chr2:52860117-52860167	HL-60	blood:	n/a
8	chr2:52856751-52856801	GM12891	blood:	n/a
9	chr2:52856495-52856545	AG10803	skin:	n/a
10	chr2:52856751-52856801	NB4	blood:	n/a
11	chr2:52860117-52860167	GM12891	blood:	n/a
12	chr2:52860117-52860167	NT2-D1	testis:	n/a
13	chr2:52857018-52857068	HMEC	breast:	n/a
14	chr2:52860117-52860167	GM12892	blood:	n/a
15	chr2:52860117-52860167	T-47D	breast:	n/a
16	chr2:52856495-52856545	A549	lung:	n/a
17	chr2:52860117-52860167	AG09309	skin:	n/a
18	chr2:52856495-52856545	HCF	heart:	n/a
19	chr2:52857018-52857068	HRCEpiC	kidney:	n/a
20	chr2:52856495-52856545	HCPEpiC	choroid plexus:	n/a
21	chr2:52857018-52857068	NH-A	brain:	n/a
22	chr2:52856918-52856968	A549	lung:	n/a
23	chr2:52857018-52857068	LNCaP	prostate:	n/a
24	chr2:52856751-52856801	GM12878	blood:	n/a
25	chr2:52860117-52860167	Hela-S3	cervix:	n/a
26	chr2:52860117-52860167	PrEC	prostate:	n/a
27	chr2:52857018-52857068	NHDF-neo	bronchial:	n/a
28	chr2:52860117-52860167	HEEpiC	esophagus:	n/a
29	chr2:52856918-52856968	MCF-7	breast:	n/a
30	chr2:52860117-52860167	NH-A	brain:	n/a
31	chr2:52860117-52860167	U87	brain:	n/a
32	chr2:52856918-52856968	HIPEpiC	eye:	n/a
33	chr2:52856751-52856801	PrEC	prostate:	n/a
34	chr2:52856751-52856801	NHBE	bronchial:	n/a
35	chr2:52860117-52860167	ECC-1	luminal epithelium:	n/a
36	chr2:52856918-52856968	Hepatocyte	liver:	n/a
37	chr2:52860117-52860167	HRCEpiC	kidney:	n/a
38	chr2:52860117-52860167	AG10803	skin:	n/a
39	chr2:52860117-52860167	HCM	heart:	n/a
40	chr2:52856495-52856545	HAEpiC	amniotic membrane:	n/a
41	chr2:52856495-52856545	IMR90	lung:	fetal
42	chr2:52856751-52856801	HUVEC	blood vessel:	n/a
43	chr2:52856495-52856545	HMEC	breast:	n/a
44	chr2:52856495-52856545	PrEC	prostate:	n/a
45	chr2:52856918-52856968	U87	brain:	n/a
46	chr2:52856751-52856801	Hela-S3	cervix:	n/a
47	chr2:52857018-52857068	ovcar-3	ovarian:	n/a
48	chr2:52857018-52857068	SKMC	muscle:	n/a
49	chr2:52856918-52856968	Caco-2	colon:	n/a
50	chr2:52856918-52856968	HNPCEpiC	eye:	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:52859439..52860286-chr4:132071047..132072003,2	MCF-7	breast:
2	chr2:52840541..52843528-chr2:52846569..52849939,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CHAC2-8	chr2:52857033-52857216	NONHSAT070675
2	lnc-CHAC2-8	chr2:52856881-52857016	NONHSAT070675

Variant related genes	Relation type
FTH1P6	TF binding region
FTH1P6	CpG island

Extended variants
information (count: 875 )
Associated
traits (count: 75 )

Variant overlapped rSNPs/rCNVs (count:875 , 50 per page) page: 1 2 3 4 5 6 7 ... 18

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs578188534	chr2:52844410-52844411	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs540937383	chr2:52844461-52844462	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs186109581	chr2:52844507-52844508	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs533407681	chr2:52844521-52844522	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs529571557	chr2:52844522-52844523	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs547914567	chr2:52844524-52844525	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs151113799	chr2:52844551-52844552	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs530521954	chr2:52844562-52844563	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs550217371	chr2:52844576-52844577	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs189392513	chr2:52844580-52844581	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs569433797	chr2:52844597-52844598	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs78916103	chr2:52844617-52844618	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs181448875	chr2:52844627-52844628	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs566685848	chr2:52844640-52844641	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs114736755	chr2:52844649-52844650	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs546687628	chr2:52844667-52844668	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs186882264	chr2:52844686-52844687	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs555525284	chr2:52844728-52844729	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs371820845	chr2:52844752-52844753	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs141115583	chr2:52844763-52844764	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs538352615	chr2:52844784-52844785	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs558250211	chr2:52844837-52844838	Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs558492474	chr2:52844893-52844894	Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs80151870	chr2:52844895-52844896	Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs540500603	chr2:52844910-52844911	Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs150239265	chr2:52844938-52844939	Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs370817520	chr2:52844956-52844957	Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs542144027	chr2:52844957-52844958	Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs138902893	chr2:52844975-52844976	Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs543305721	chr2:52844988-52844989	Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs143484726	chr2:52844998-52844999	Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs191731267	chr2:52845006-52845007	Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs373869600	chr2:52845025-52845026	Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs183237837	chr2:52845065-52845066	Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs145877499	chr2:52845069-52845070	Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs76714526	chr2:52845083-52845084	Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs74990967	chr2:52845094-52845095	Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs541446596	chr2:52845132-52845133	Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs529176773	chr2:52845134-52845135	Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs186529240	chr2:52845145-52845146	Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs374601699	chr2:52845164-52845165	Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs555311631	chr2:52845206-52845207	Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs189661835	chr2:52845208-52845209	Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs558162375	chr2:52845238-52845239	Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs550399738	chr2:52845240-52845241	Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs534293466	chr2:52845244-52845245	Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs554120183	chr2:52845311-52845312	Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs574134937	chr2:52845326-52845327	Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs542963738	chr2:52845334-52845335	Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs556410411	chr2:52845376-52845377	Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:75)

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
Lung cancer	17297452	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Ovarian cancer	21720365	CNVD
abnormal development	18461090	CNVD
Lung adenocarcinoma	17086460	CNVD
Retinoblastoma	22278416	CNVD
Cancer	21183584	CNVD
Breast cancer	16397240	CNVD
Acute lymphoblastic leukemia	18768390	CNVD
Mental retardation	19521722	CNVD
Schizophrenia	18990708	CNVD
Schizophrenia	18940311	CNVD
Schizophrenia	19348701	CNVD
Schizophrenia	18945720	CNVD
Schizophrenia	19571808	CNVD
Prostate cancer	16573809	CNVD
Neuroticism	17667963	CNVD
Schizophrenia	19443537	CNVD
Schizophrenia	19546859	CNVD
Autism	17322880	CNVD
Lung cancer	17086460	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
Myelofibrosis	22110671	CNVD
Schizophrenia	23813976	CNVD

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:52839400-52844600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr2:52840600-52844800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr2:52844400-52845200	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr2:52844600-52845000	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr2:52844800-52845200	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr2:52844800-52845400	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr2:52844800-52845600	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr2:52846000-52846600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr2:52846600-52847800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr2:52847600-52848800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr2:52847800-52850600	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr2:52848000-52848200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr2:52848400-52848800	Enhancers	Brain Cingulate Gyrus	brain
14	chr2:52848800-52849200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr2:52848800-52849200	Weak transcription	Brain Cingulate Gyrus	brain
16	chr2:52849200-52850000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr2:52849200-52850000	Enhancers	Brain Cingulate Gyrus	brain
18	chr2:52849400-52849600	Enhancers	Left Ventricle	heart
19	chr2:52865200-52867000	Enhancers	Fetal Heart	heart
20	chr2:52871200-52872200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr2:52874000-52875200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr2:52874600-52874800	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr2:52874600-52875400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
24	chr2:52874600-52875800	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
25	chr2:52874800-52876000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr2:52878400-52878600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr2:52878600-52884800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr2:52885400-52887000	Enhancers	NH-A	brain

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