Variant report

Variant	nsv3906
Chromosome Location	chr3:88609226-88654550
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	BACH1	chr3:88638381-88638592	H1-hESC	embryonic stem cell:	n/a	n/a
2	CEBPB	chr3:88653672-88654202	Hela-S3	cervix:	n/a	n/a
3	CEBPB	chr3:88616794-88617068	HepG2	liver:	n/a	chr3:88616925-88616936
4	CEBPB	chr3:88633331-88633652	HepG2	liver:	n/a	n/a
5	CEBPB	chr3:88649252-88649556	HepG2	liver:	n/a	chr3:88649410-88649421
6	CEBPB	chr3:88649230-88649597	Hela-S3	cervix:	n/a	chr3:88649410-88649421
7	CEBPB	chr3:88616744-88617070	IMR90	lung:	n/a	chr3:88616925-88616936
8	CEBPB	chr3:88633365-88633658	A549	lung:	n/a	n/a
9	CTCF	chr3:88615609-88615675	Lung_OC	lung:	n/a	n/a
10	CTCF	chr3:88613141-88613193	GM20000	blood:	n/a	n/a
11	E2F4	chr3:88619047-88619169	MCF10A-Er-Src	breast:	n/a	n/a
12	E2F4	chr3:88653480-88653680	MCF10A-Er-Src	breast:	n/a	n/a
13	EP300	chr3:88639859-88639911	GM12878	blood:	n/a	n/a
14	FAM48A	chr3:88636386-88636470	GM12878	blood:	n/a	n/a
15	FOS	chr3:88622640-88622999	MCF10A-Er-Src	breast:	n/a	chr3:88622844-88622854 chr3:88622844-88622854 chr3:88622844-88622854
16	FOS	chr3:88645733-88645924	MCF10A-Er-Src	breast:	n/a	n/a
17	FOS	chr3:88622666-88623021	MCF10A-Er-Src	breast:	n/a	chr3:88622844-88622854 chr3:88622844-88622854 chr3:88622844-88622854
18	FOS	chr3:88642507-88642700	MCF10A-Er-Src	breast:	n/a	n/a
19	FOS	chr3:88622620-88622988	MCF10A-Er-Src	breast:	n/a	chr3:88622844-88622854 chr3:88622844-88622854 chr3:88622844-88622854
20	FOS	chr3:88622678-88622951	MCF10A-Er-Src	breast:	n/a	chr3:88622844-88622854 chr3:88622844-88622854 chr3:88622844-88622854
21	FOS	chr3:88653760-88653828	MCF10A-Er-Src	breast:	n/a	n/a
22	GATA3	chr3:88639599-88639787	SH-SY5Y	brain:	n/a	n/a
23	IRF1	chr3:88616882-88616890	K562	blood:	n/a	n/a
24	JUND	chr3:88638916-88639144	HepG2	liver:	n/a	chr3:88638969-88638980
25	JUND	chr3:88612089-88612094	H1-hESC	embryonic stem cell:	n/a	n/a
26	MAFF	chr3:88645170-88645284	HepG2	liver:	n/a	n/a
27	MAFF	chr3:88640127-88640191	HepG2	liver:	n/a	chr3:88640164-88640182
28	MAFK	chr3:88640046-88640274	HepG2	liver:	n/a	chr3:88640166-88640182 chr3:88640166-88640177 chr3:88640165-88640179 chr3:88640166-88640177 chr3:88640167-88640178
29	MAFK	chr3:88638371-88638486	HepG2	liver:	n/a	n/a
30	MAFK	chr3:88645643-88645884	HepG2	liver:	n/a	chr3:88645792-88645801 chr3:88645791-88645801
31	MAFK	chr3:88638849-88639078	HepG2	liver:	n/a	chr3:88638967-88638983 chr3:88638968-88638982 chr3:88638965-88638985 chr3:88638964-88638979
32	MAFK	chr3:88640010-88640209	HepG2	liver:	n/a	chr3:88640166-88640182 chr3:88640166-88640177 chr3:88640165-88640179 chr3:88640166-88640177 chr3:88640167-88640178
33	MAFK	chr3:88638316-88638560	H1-hESC	embryonic stem cell:	n/a	chr3:88638482-88638491 chr3:88638480-88638496 chr3:88638485-88638496 chr3:88638484-88638495 chr3:88638483-88638497 chr3:88638485-88638496
34	MAFK	chr3:88615593-88615644	IMR90	lung:	n/a	n/a
35	MAFK	chr3:88638876-88639095	IMR90	lung:	n/a	chr3:88638967-88638983 chr3:88638968-88638982 chr3:88638965-88638985 chr3:88638964-88638979
36	MAFK	chr3:88638831-88639155	HepG2	liver:	n/a	chr3:88638967-88638983 chr3:88638968-88638982 chr3:88638965-88638985 chr3:88638964-88638979
37	MAFK	chr3:88638353-88638519	HepG2	liver:	n/a	chr3:88638482-88638491 chr3:88638480-88638496 chr3:88638485-88638496 chr3:88638484-88638495 chr3:88638483-88638497 chr3:88638485-88638496
38	MAFK	chr3:88645169-88645310	HepG2	liver:	n/a	n/a
39	MAX	chr3:88632724-88632734	HepG2	liver:	n/a	n/a
40	MYC	chr3:88640186-88640260	H1-hESC	embryonic stem cell:	n/a	n/a
41	MYC	chr3:88649109-88649309	MCF10A-Er-Src	breast:	n/a	n/a
42	NFATC1	chr3:88628565-88628841	GM12878	blood:	n/a	n/a
43	NFIC	chr3:88644059-88644703	ECC-1	luminal epithelium:	n/a	n/a
44	NFIC	chr3:88643979-88644753	ECC-1	luminal epithelium:	n/a	n/a
45	POLR2A	chr3:88633578-88633775	MCF10A-Er-Src	breast:	n/a	n/a
46	POLR2A	chr3:88645397-88645539	MCF10A-Er-Src	breast:	n/a	n/a
47	POLR2A	chr3:88644015-88644595	SK-N-MC	brain:	n/a	n/a
48	POLR2A	chr3:88628729-88628807	MCF10A-Er-Src	breast:	n/a	n/a
49	POLR2A	chr3:88628887-88628961	MCF10A-Er-Src	breast:	n/a	n/a
50	POLR2A	chr3:88629161-88629172	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:88630638..88632536-chr3:88637327..88639370,2	K562	blood:
2	chr3:88637113..88639564-chr3:88641167..88643213,2	MCF-7	breast:
3	chr3:88630638..88632536-chr3:88637327..88639370,2	K562	blood:
4	chr3:88637113..88639564-chr3:88641167..88643213,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C3orf38-5	chr3:88650211-88650552	NONHSAT090709

Variant related genes	Relation type
NDUFA5P5	TF binding region

Extended variants
information (count: 672 )
Associated
traits (count: 71 )

Variant overlapped rSNPs/rCNVs (count:672 , 50 per page) page: 1 2 3 4 5 6 7 ... 14

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs375513328	chr3:88612841-88612842	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
2	rs111538925	chr3:88612864-88612865	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
3	rs577999942	chr3:88612884-88612885	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
4	rs544671933	chr3:88612891-88612892	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
5	rs116701492	chr3:88612954-88612955	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
6	rs578152278	chr3:88612958-88612959	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
7	rs151164625	chr3:88613005-88613006	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
8	rs575480233	chr3:88613011-88613012	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
9	rs565619710	chr3:88613057-88613058	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
10	rs368804701	chr3:88613063-88613064	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
11	rs543578176	chr3:88613095-88613096	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
12	rs562194305	chr3:88613111-88613112	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
13	rs191197683	chr3:88613140-88613141	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
14	rs182316974	chr3:88613170-88613171	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
15	rs186714789	chr3:88613171-88613172	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
16	rs529313358	chr3:88613185-88613186	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
17	rs147644046	chr3:88622023-88622024	Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs534453951	chr3:88622032-88622033	Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs116492009	chr3:88622033-88622034	Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs577342279	chr3:88622050-88622051	Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs113558414	chr3:88622056-88622057	Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs80176787	chr3:88622077-88622078	Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs572430962	chr3:88622087-88622088	Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs112125668	chr3:88622099-88622100	Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs145526109	chr3:88622118-88622119	Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs541426700	chr3:88622192-88622193	Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs536386843	chr3:88622201-88622202	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs144339775	chr3:88622211-88622212	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs181617164	chr3:88622252-88622253	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs541650421	chr3:88622263-88622264	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs62269512	chr3:88622287-88622288	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
32	rs575193498	chr3:88622365-88622366	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs550834652	chr3:88622374-88622375	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs186511476	chr3:88622400-88622401	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs530172086	chr3:88622446-88622447	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs548613504	chr3:88622499-88622500	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs566838506	chr3:88622521-88622522	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs545801261	chr3:88622539-88622540	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs191027669	chr3:88622540-88622541	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs564180216	chr3:88622541-88622542	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs112919081	chr3:88622560-88622561	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs552816664	chr3:88622561-88622562	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs181389365	chr3:88622564-88622565	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs561463097	chr3:88622568-88622569	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs373736904	chr3:88622599-88622600	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs113197980	chr3:88622605-88622606	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs72921984	chr3:88622638-88622639	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
48	rs540398515	chr3:88622699-88622700	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs113759459	chr3:88622716-88622717	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs529480349	chr3:88622748-88622749	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:71)

Disease	PMID	Source
Insulin resistance	16721378	CNVD
Neuroblastoma	18664255	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Multiple myeloma	17077331	CNVD
Oral squamous cell carcinoma	17134496	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
Acute myeloid leukemia	20729466	CNVD
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Glioblastoma multiforme	21080181	CNVD
Retinoblastoma	21504564	CNVD
Renal cell carcinoma	21668985	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Breast cancer	17603634	CNVD
Uveal melanoma	20484589	CNVD
Autism	22495311	CNVD
Lung cancer	18438408	CNVD
Hirschsprung''s Disease	21712996	CNVD
Hepatocellular carcinoma	16750200	CNVD
Cancer	21183584	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Bipolar disorder	20877625	CNVD
Bipolar disorder	21956041	CNVD
Bipolar disorder	22241247	CNVD
Biliary cancer	18923514	CNVD
Prostate cancer	21965145	CNVD
Cancer	21129771	CNVD
Congenital diaphragmatic hernia	21085971	CNVD
Cervical cancer	21062161	CNVD
Squamous cell cancer	20885788	CNVD
Melanoma	18172304	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Metanephric adenoma	20802469	CNVD
Bipolar disorder	18458673	CNVD
Breast cancer	22032731	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Wilms tumour	21544195	CNVD
Soft tissue tumor	16732325	CNVD
small cell lung cancer	20016488	CNVD
Neurodevelopmental disorder	22521361	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
craniofacial dysmorphism	21918468	CNVD
Cancer	20164920	CNVD
Non-small cell lung cancer	21829676	CNVD
Lung cancer	19547694	CNVD
Cancer	20164919	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:88612800-88613200	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:88612800-88613200	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:88612800-88613200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:88622000-88622200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:88622000-88622200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr3:88622000-88622800	Enhancers	HMEC	breast
7	chr3:88622200-88623400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:88622400-88627800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr3:88622600-88622800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr3:88622600-88623000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr3:88622600-88623000	Enhancers	Pancreatic Islets	Pancreatic Islet
12	chr3:88622800-88623600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr3:88623000-88623200	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr3:88623200-88624000	Enhancers	Pancreatic Islets	Pancreatic Islet
15	chr3:88623400-88623600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr3:88623400-88623800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:88623800-88627800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:88627800-88628200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:88627800-88628200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr3:88637000-88637400	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr3:88637400-88637800	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr3:88637400-88638600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr3:88637800-88638000	Enhancers	Brain Germinal Matrix	brain
24	chr3:88637800-88640000	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr3:88637800-88640000	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr3:88638000-88638600	Enhancers	iPS-18 Cell Line	embryonic stem cell
27	chr3:88638000-88639600	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr3:88638000-88640000	Enhancers	iPS-15b Cell Line	embryonic stem cell
29	chr3:88638200-88638800	Enhancers	HUES6 Cell Line	embryonic stem cell
30	chr3:88638200-88639200	Weak transcription	Brain Germinal Matrix	brain
31	chr3:88638400-88640000	Enhancers	iPS-20b Cell Line	embryonic stem cell
32	chr3:88638600-88639000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr3:88639000-88639400	Enhancers	iPS-18 Cell Line	embryonic stem cell
34	chr3:88639200-88640000	Enhancers	Brain Germinal Matrix	brain
35	chr3:88639400-88640000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr3:88640000-88644600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr3:88644600-88646000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr3:88645000-88646400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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