Variant report

Variant	nsv523804
Chromosome Location	chr2:52503364-52553023
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	chr2:52508157-52508457	HepG2	liver:	n/a	chr2:52508316-52508327
2	CEBPB	chr2:52516375-52516634	IMR90	lung:	n/a	chr2:52516470-52516481
3	CEBPB	chr2:52508166-52508428	IMR90	lung:	n/a	chr2:52508316-52508327
4	CEBPB	chr2:52516875-52517234	Hela-S3	cervix:	n/a	n/a
5	CEBPB	chr2:52516890-52517212	IMR90	lung:	n/a	n/a
6	CEBPB	chr2:52516417-52516634	HepG2	liver:	n/a	chr2:52516470-52516481
7	CTCF	chr2:52510140-52510290	HAc	cerebellar:	n/a	n/a
8	CTCF	chr2:52549827-52549833	GM20000	blood:	n/a	n/a
9	CTCF	chr2:52535760-52535910	GM12865	blood:	n/a	n/a
10	CTCF	chr2:52524865-52524936	Lung_OC	lung:	n/a	n/a
11	FOS	chr2:52546071-52546265	MCF10A-Er-Src	breast:	n/a	chr2:52546159-52546169 chr2:52546159-52546169 chr2:52546159-52546169 chr2:52546159-52546169 chr2:52546160-52546169
12	FOS	chr2:52517056-52517213	MCF10A-Er-Src	breast:	n/a	n/a
13	FOS	chr2:52546119-52546263	MCF10A-Er-Src	breast:	n/a	chr2:52546159-52546169 chr2:52546159-52546169 chr2:52546159-52546169 chr2:52546159-52546169 chr2:52546160-52546169
14	GATA3	chr2:52526582-52526776	SH-SY5Y	brain:	n/a	n/a
15	JUND	chr2:52552473-52552686	HepG2	liver:	n/a	n/a
16	MAFF	chr2:52517644-52517935	HepG2	liver:	n/a	chr2:52517785-52517803
17	MAFK	chr2:52517627-52517927	HepG2	liver:	n/a	n/a
18	MAFK	chr2:52540342-52540568	HepG2	liver:	n/a	n/a
19	MAFK	chr2:52517736-52517834	IMR90	lung:	n/a	n/a
20	MAFK	chr2:52505046-52505180	HepG2	liver:	n/a	n/a
21	MAZ	chr2:52534638-52534721	HepG2	liver:	n/a	n/a
22	MAZ	chr2:52505853-52505864	HepG2	liver:	n/a	n/a
23	MYC	chr2:52544612-52544649	H1-hESC	embryonic stem cell:	n/a	n/a
24	NANOG	chr2:52539014-52539295	H1-hESC	embryonic stem cell:	n/a	n/a
25	NANOG	chr2:52538956-52539344	H1-hESC	embryonic stem cell:	n/a	n/a
26	NFYB	chr2:52536525-52536729	GM12878	blood:	n/a	n/a
27	POLR2A	chr2:52505923-52506034	MCF10A-Er-Src	breast:	n/a	n/a
28	POLR2A	chr2:52517001-52517067	MCF10A-Er-Src	breast:	n/a	n/a
29	POLR2A	chr2:52513840-52513938	ProgFib	skin:	n/a	n/a
30	POLR2A	chr2:52507222-52507570	MCF10A-Er-Src	breast:	n/a	n/a
31	POLR2A	chr2:52529424-52529501	HUVEC	blood vessel:	n/a	n/a
32	POLR2A	chr2:52534666-52534727	MCF10A-Er-Src	breast:	n/a	n/a
33	POU5F1	chr2:52539032-52539326	H1-hESC	embryonic stem cell:	n/a	n/a
34	STAT3	chr2:52507357-52507557	MCF10A-Er-Src	breast:	n/a	n/a
35	STAT3	chr2:52524812-52524826	MCF10A-Er-Src	breast:	n/a	n/a
36	STAT3	chr2:52546147-52546318	MCF10A-Er-Src	breast:	n/a	n/a
37	STAT3	chr2:52547264-52547598	MCF10A-Er-Src	breast:	n/a	n/a
38	TAL1	chr2:52518039-52518102	K562	blood:	n/a	n/a
39	ZNF143	chr2:52506493-52506860	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:52521422..52524399-chr2:52528510..52532522,3	K562	blood:
2	chr2:52521422..52524399-chr2:52528510..52532522,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CHAC2-4	chr2:52543370-52543438	ENSG00000231918.1

Variant related genes	Relation type
ENSG00000202195	TF binding region

Extended variants
information (count: 775 )
Associated
traits (count: 83 )

Variant overlapped rSNPs/rCNVs (count:775 , 50 per page) page: 1 2 3 4 5 6 7 ... 16

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs13417515	chr2:52503364-52503365	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs149243545	chr2:52503394-52503395	Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs570826480	chr2:52503407-52503408	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs78274460	chr2:52503424-52503425	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs558356115	chr2:52503425-52503426	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs79373404	chr2:52503433-52503434	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs193012294	chr2:52503442-52503443	Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs534493109	chr2:52503459-52503460	Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs552519443	chr2:52503465-52503466	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs77639472	chr2:52503489-52503490	Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs148431630	chr2:52503513-52503514	Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs79547550	chr2:52503547-52503548	Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs10711460	chr2:52503587-52503588	Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs561406413	chr2:52503602-52503603	Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs575314747	chr2:52503603-52503604	Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs35066506	chr2:52503624-52503625	Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs142538465	chr2:52503642-52503643	Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs72885555	chr2:52503651-52503652	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
19	rs536564835	chr2:52503656-52503657	Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs368298733	chr2:52503658-52503659	Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs72798361	chr2:52503675-52503676	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
22	rs72885557	chr2:52503682-52503683	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
23	rs529262549	chr2:52503706-52503707	Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs112392958	chr2:52503708-52503709	Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs546092882	chr2:52503709-52503710	Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs574158025	chr2:52503763-52503764	Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs372792688	chr2:52503764-52503765	Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs185198873	chr2:52503775-52503776	Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs538317570	chr2:52503820-52503821	Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs188813527	chr2:52503827-52503828	Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs551621158	chr2:52503832-52503833	Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs571805126	chr2:52503864-52503865	Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs534176025	chr2:52503865-52503866	Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs144554151	chr2:52503868-52503869	Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs192702848	chr2:52503911-52503912	Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs535049505	chr2:52503921-52503922	Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs554965029	chr2:52503952-52503953	Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs575164934	chr2:52503991-52503992	Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs376086726	chr2:52504003-52504004	Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs368056458	chr2:52504007-52504008	Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs544284115	chr2:52504051-52504052	Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs184101251	chr2:52504072-52504073	Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs577718220	chr2:52504076-52504077	Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs540434821	chr2:52504083-52504084	Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs571091888	chr2:52504124-52504125	Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs188104009	chr2:52504185-52504186	Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs74927148	chr2:52504191-52504192	Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs562889254	chr2:52504212-52504213	Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs72885559	chr2:52504225-52504226	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
50	rs551852210	chr2:52504258-52504259	Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:83)

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
small cell lung cancer	20016488	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
Schizophrenia	20433910	CNVD
Autism	21701786	CNVD
Attention deficit hyperactivity disorder	21324949	CNVD
Austim spectrum disorder	21302340	CNVD
Schizophrenia	20587603	CNVD
Schizophrenia	20553308	CNVD
Autism	22241247	CNVD
Myelofibrosis	22110671	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
Pancreatic ductal adenocarcinoma	19077451	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:52503200-52504200	Enhancers	HUES64 Cell Line	embryonic stem cell
2	chr2:52503200-52504400	Enhancers	HUES6 Cell Line	embryonic stem cell
3	chr2:52503600-52504400	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr2:52503800-52504200	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr2:52513400-52514000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr2:52513400-52515400	Enhancers	Fetal Intestine Small	intestine
7	chr2:52513400-52516400	Enhancers	Fetal Intestine Large	intestine
8	chr2:52513600-52514000	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr2:52513600-52514200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr2:52513600-52514400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:52513600-52516000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr2:52513800-52514000	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr2:52514200-52516400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr2:52514400-52515200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:52514600-52515200	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr2:52514600-52515400	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr2:52514800-52515400	Enhancers	iPS-20b Cell Line	embryonic stem cell
18	chr2:52515200-52515400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:52515200-52523000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr2:52515400-52516400	Weak transcription	Fetal Intestine Small	intestine
21	chr2:52515800-52516400	Enhancers	Fetal Heart	heart
22	chr2:52516000-52519800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr2:52516400-52516600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr2:52516400-52516600	Enhancers	Fetal Intestine Small	intestine
25	chr2:52519000-52519200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr2:52519000-52520800	Enhancers	HUES48 Cell Line	embryonic stem cell
27	chr2:52519200-52520200	Enhancers	H1 Cell Line	embryonic stem cell
28	chr2:52519200-52520200	Enhancers	iPS-20b Cell Line	embryonic stem cell
29	chr2:52519200-52521600	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr2:52519600-52520600	Enhancers	iPS-18 Cell Line	embryonic stem cell
31	chr2:52519600-52520800	Enhancers	HUES64 Cell Line	embryonic stem cell
32	chr2:52519800-52521000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr2:52520000-52520200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr2:52520000-52521200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr2:52520200-52521400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr2:52520600-52521600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr2:52520800-52521200	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr2:52520800-52522400	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr2:52521000-52522400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr2:52521200-52523800	Enhancers	HUES48 Cell Line	embryonic stem cell
41	chr2:52521400-52522000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr2:52521400-52522200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr2:52521600-52522200	Enhancers	iPS-18 Cell Line	embryonic stem cell
44	chr2:52521600-52524800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr2:52522200-52522800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr2:52522400-52523000	Enhancers	HUES64 Cell Line	embryonic stem cell
47	chr2:52522800-52523000	Enhancers	iPS-18 Cell Line	embryonic stem cell
48	chr2:52522800-52523200	Enhancers	HUES6 Cell Line	embryonic stem cell
49	chr2:52523000-52523800	Enhancers	iPS-15b Cell Line	embryonic stem cell
50	chr2:52524800-52526000	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell

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