Variant report

Variant	nsv874123
Chromosome Location	chr2:52706489-52730021
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	chr2:52706340-52706490	AG04450	lung:	n/a	n/a
2	CTCF	chr2:52706560-52706710	HEEpiC	esophagus:	n/a	n/a
3	CTCF	chr2:52706340-52706490	HEEpiC	esophagus:	n/a	n/a
4	E2F4	chr2:52726538-52726745	MCF10A-Er-Src	breast:	n/a	n/a
5	E2F4	chr2:52716051-52716210	MCF10A-Er-Src	breast:	n/a	n/a
6	EP300	chr2:52725664-52725727	GM12878	blood:	n/a	n/a
7	GATA3	chr2:52719241-52719532	SH-SY5Y	brain:	n/a	n/a
8	IRF3	chr2:52713294-52713305	GM12878	blood:	n/a	n/a
9	JUN	chr2:52722986-52723289	K562	blood:	n/a	n/a
10	JUN	chr2:52721276-52721322	HepG2	liver:	n/a	n/a
11	MAFF	chr2:52721437-52721549	HepG2	liver:	n/a	n/a
12	MAFK	chr2:52713147-52713257	IMR90	lung:	n/a	chr2:52713158-52713169 chr2:52713153-52713169 chr2:52713157-52713168 chr2:52713158-52713169 chr2:52713153-52713168
13	MAFK	chr2:52721404-52721556	HepG2	liver:	n/a	n/a
14	MAFK	chr2:52721401-52721622	HepG2	liver:	n/a	n/a
15	MAFK	chr2:52713114-52713271	HepG2	liver:	n/a	chr2:52713158-52713169 chr2:52713153-52713169 chr2:52713157-52713168 chr2:52713158-52713169 chr2:52713153-52713168
16	MAFK	chr2:52713039-52713209	HepG2	liver:	n/a	chr2:52713158-52713169 chr2:52713153-52713169 chr2:52713157-52713168 chr2:52713158-52713169 chr2:52713153-52713168
17	MAFK	chr2:52707497-52707683	HepG2	liver:	n/a	n/a
18	POLR2A	chr2:52707308-52707474	MCF10A-Er-Src	breast:	n/a	n/a
19	POLR2A	chr2:52707015-52707034	MCF10A-Er-Src	breast:	n/a	n/a
20	POLR2A	chr2:52720346-52720500	MCF10A-Er-Src	breast:	n/a	n/a
21	RAD21	chr2:52706242-52706552	H1-hESC	embryonic stem cell:	n/a	n/a
22	SPI1	chr2:52725541-52725858	GM12878	blood:	n/a	n/a
23	SPI1	chr2:52725544-52725776	GM12891	blood:	n/a	n/a
24	SPI1	chr2:52725514-52725796	GM12891	blood:	n/a	n/a
25	SPI1	chr2:52706565-52706786	HL-60	blood:	n/a	n/a
26	STAT3	chr2:52723592-52723863	MCF10A-Er-Src	breast:	n/a	chr2:52723770-52723777
27	STAT3	chr2:52708548-52708556	MCF10A-Er-Src	breast:	n/a	n/a
28	STAT3	chr2:52710658-52710858	MCF10A-Er-Src	breast:	n/a	n/a
29	STAT3	chr2:52727658-52727810	MCF10A-Er-Src	breast:	n/a	n/a
30	STAT3	chr2:52707741-52707863	MCF10A-Er-Src	breast:	n/a	n/a
31	STAT3	chr2:52714125-52714316	MCF10A-Er-Src	breast:	n/a	n/a
32	TEAD4	chr2:52706142-52706582	H1-hESC	embryonic stem cell:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ASB3-3	chr2:52722903-52722974	XLOC_002095
2	lnc-ASB3-3	chr2:52721826-52722000	XLOC_002095
3	lnc-ASB3-3	chr2:52727682-52727890	XLOC_002095
4	lnc-ASB3-3	chr2:52725741-52725923	XLOC_002095

Variant related genes	Relation type
ENSG00000225842	TF binding region
ENSG00000236837	TF binding region
RABEP1	miRNA target sites
RAD23B	miRNA target sites
RAB9B	miRNA target sites

Extended variants
information (count: 401 )
Associated
traits (count: 78 )

Variant overlapped rSNPs/rCNVs (count:401 , 50 per page) page: 1 2 3 4 5 6 7 ... 9

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs13407104	chr2:52706489-52706490	Inactive region	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs369055629	chr2:52706494-52706495	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
3	rs373487791	chr2:52706498-52706499	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
4	rs548140973	chr2:52706542-52706543	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
5	rs6760658	chr2:52721889-52721890	Inactive region	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
6	rs183134793	chr2:52721891-52721892	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
7	rs373846948	chr2:52721898-52721899	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
8	rs548303190	chr2:52721926-52721927	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
9	rs187124321	chr2:52721936-52721937	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
10	rs570235571	chr2:52721991-52721992	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
11	rs528365748	chr2:52722806-52722807	Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs548326664	chr2:52722815-52722816	Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs116495765	chr2:52722817-52722818	Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs141406683	chr2:52722833-52722834	Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs4971836	chr2:52722835-52722836	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
16	rs145282772	chr2:52722849-52722850	Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs185616967	chr2:52722864-52722865	Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs72892924	chr2:52722885-52722886	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
19	rs368269216	chr2:52722886-52722887	Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs146421197	chr2:52722894-52722895	Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs571222732	chr2:52722898-52722899	Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs536113717	chr2:52722902-52722903	Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs552900930	chr2:52722922-52722923	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
24	rs574440522	chr2:52722932-52722933	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
25	rs527392277	chr2:52722934-52722935	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
26	rs548989745	chr2:52722971-52722972	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
27	rs17043033	chr2:52722976-52722977	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
28	rs190487733	chr2:52722981-52722982	Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs117953477	chr2:52722988-52722989	Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs375246615	chr2:52722996-52722997	Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs72892927	chr2:52723020-52723021	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
32	rs114628095	chr2:52723026-52723027	Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs4971606	chr2:52723031-52723032	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
34	rs542078364	chr2:52723068-52723069	Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs561939286	chr2:52723109-52723110	Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs140955476	chr2:52723112-52723113	Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs544188847	chr2:52723128-52723129	Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs570963693	chr2:52723147-52723148	Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs368789731	chr2:52723155-52723156	Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs538418837	chr2:52723163-52723164	Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs150415195	chr2:52723198-52723199	Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs193118588	chr2:52723232-52723233	Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs546896284	chr2:52723320-52723321	Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs567029438	chr2:52723321-52723322	Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs150115265	chr2:52723334-52723335	Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs572403043	chr2:52723351-52723352	Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs138421506	chr2:52723367-52723368	Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs184488168	chr2:52723373-52723374	Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs17733177	chr2:52723375-52723376	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
50	rs76008555	chr2:52723385-52723386	Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:78)

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
Non-syndromic sensorineural hearing loss	18451855	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
small cell lung cancer	20016488	CNVD
Myelofibrosis	22110671	CNVD
Breast cancer	22522925	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:52722800-52723800	Enhancers	Liver	Liver
2	chr2:52723800-52724600	Weak transcription	Liver	Liver
3	chr2:52724600-52725800	ZNF genes & repeats	Liver	Liver
4	chr2:52725800-52727200	Weak transcription	Liver	Liver
5	chr2:52727200-52730600	Enhancers	Liver	Liver
6	chr2:52727400-52729600	Enhancers	Fetal Heart	heart
7	chr2:52727600-52728600	Enhancers	Pancreatic Islets	Pancreatic Islet
8	chr2:52727600-52729800	Enhancers	Fetal Lung	lung
9	chr2:52727800-52728000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr2:52728000-52728600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr2:52728600-52729400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr2:52728800-52729600	Enhancers	Fetal Intestine Small	intestine
13	chr2:52728800-52729600	Enhancers	Left Ventricle	heart
14	chr2:52728800-52729600	Enhancers	Pancreas	Pancrea
15	chr2:52728800-52730400	Enhancers	Fetal Intestine Large	intestine

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