Variant report

Variant	nsv1008716
Chromosome Location	chr4:21580423-21633636
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	chr4:21599919-21600143	IMR90	lung:	n/a	chr4:21600032-21600043
2	CEBPB	chr4:21630812-21631085	IMR90	lung:	n/a	chr4:21630944-21630955 chr4:21630944-21630957
3	CEBPB	chr4:21617958-21618186	HepG2	liver:	n/a	chr4:21618067-21618078
4	CEBPB	chr4:21630849-21631084	HepG2	liver:	n/a	chr4:21630944-21630955 chr4:21630944-21630957
5	CEBPB	chr4:21599831-21600217	HepG2	liver:	n/a	chr4:21600032-21600043
6	CEBPB	chr4:21629752-21630097	H1-hESC	embryonic stem cell:	n/a	n/a
7	CEBPB	chr4:21610496-21610650	H1-hESC	embryonic stem cell:	n/a	n/a
8	CEBPB	chr4:21629770-21630096	HepG2	liver:	n/a	n/a
9	CTCF	chr4:21607168-21607201	Lung_OC	lung:	n/a	n/a
10	CTCF	chr4:21600620-21600770	BE2_C	brain:	n/a	n/a
11	CTCF	chr4:21631959-21632006	GM20000	blood:	n/a	n/a
12	CTCF	chr4:21583526-21583759	K562	blood:	n/a	n/a
13	E2F4	chr4:21583518-21583741	MCF10A-Er-Src	breast:	n/a	n/a
14	E2F4	chr4:21586573-21586719	MCF10A-Er-Src	breast:	n/a	n/a
15	E2F4	chr4:21628565-21628598	MCF10A-Er-Src	breast:	n/a	n/a
16	EP300	chr4:21619143-21619433	SK-N-SH_RA	brain:	n/a	chr4:21619358-21619368
17	EP300	chr4:21594787-21595389	SK-N-SH_RA	brain:	n/a	chr4:21595171-21595180 chr4:21595172-21595181
18	EP300	chr4:21594663-21595467	SK-N-SH	brain:	n/a	chr4:21595171-21595180 chr4:21595172-21595181
19	EP300	chr4:21583623-21583740	GM12878	blood:	n/a	n/a
20	EP300	chr4:21594667-21595475	SK-N-SH_RA	brain:	n/a	chr4:21595171-21595180 chr4:21595172-21595181
21	EP300	chr4:21598139-21598531	H1-hESC	embryonic stem cell:	n/a	chr4:21598474-21598488 chr4:21598263-21598277 chr4:21598485-21598499 chr4:21598355-21598365
22	FOS	chr4:21616445-21616603	MCF10A-Er-Src	breast:	n/a	n/a
23	FOS	chr4:21616508-21616633	MCF10A-Er-Src	breast:	n/a	n/a
24	FOS	chr4:21630936-21630989	MCF10A-Er-Src	breast:	n/a	n/a
25	FOSL2	chr4:21594906-21595417	SK-N-SH	brain:	n/a	chr4:21595171-21595181 chr4:21595172-21595179 chr4:21595171-21595180 chr4:21595172-21595180
26	GATA2	chr4:21622782-21623130	HUVEC	blood vessel:	n/a	n/a
27	GATA3	chr4:21619822-21620098	SH-SY5Y	brain:	n/a	chr4:21620055-21620065 chr4:21620055-21620064
28	GATA3	chr4:21583519-21583886	SH-SY5Y	brain:	n/a	n/a
29	GATA3	chr4:21594601-21595536	SK-N-SH	brain:	n/a	chr4:21595187-21595208
30	GATA3	chr4:21593813-21593987	SH-SY5Y	brain:	n/a	n/a
31	GATA3	chr4:21594632-21595465	SK-N-SH	brain:	n/a	chr4:21595187-21595208
32	IRF1	chr4:21583518-21583886	K562	blood:	n/a	n/a
33	IRF3	chr4:21621452-21621463	GM12878	blood:	n/a	n/a
34	JUN	chr4:21611985-21612166	HepG2	liver:	n/a	chr4:21612057-21612070
35	JUND	chr4:21600021-21600122	HepG2	liver:	n/a	n/a
36	JUND	chr4:21611980-21612096	HepG2	liver:	n/a	n/a
37	JUND	chr4:21583575-21583787	A549	lung:	n/a	n/a
38	JUND	chr4:21595018-21595182	HepG2	liver:	n/a	chr4:21595170-21595181 chr4:21595171-21595181 chr4:21595172-21595179 chr4:21595171-21595180 chr4:21595172-21595180
39	JUND	chr4:21594769-21595415	SK-N-SH	brain:	n/a	chr4:21595170-21595181 chr4:21595171-21595181 chr4:21595172-21595179 chr4:21595171-21595180 chr4:21595172-21595180
40	KAP1	chr4:21592614-21593060	K562	blood:	n/a	n/a
41	MAFF	chr4:21627354-21627587	HepG2	liver:	n/a	chr4:21627415-21627433
42	MAFF	chr4:21626866-21626998	K562	blood:	n/a	n/a
43	MAFF	chr4:21626796-21627058	HepG2	liver:	n/a	n/a
44	MAFK	chr4:21627291-21627541	HepG2	liver:	n/a	chr4:21627417-21627428 chr4:21627417-21627432 chr4:21627417-21627433 chr4:21627418-21627429 chr4:21627416-21627430 chr4:21627417-21627428 chr4:21627418-21627429
45	MAFK	chr4:21616308-21616538	HepG2	liver:	n/a	chr4:21616398-21616409 chr4:21616398-21616409
46	MAFK	chr4:21616254-21616562	HepG2	liver:	n/a	chr4:21616398-21616409 chr4:21616398-21616409
47	MAFK	chr4:21626806-21627054	K562	blood:	n/a	n/a
48	MAFK	chr4:21626840-21627046	HepG2	liver:	n/a	n/a
49	MAFK	chr4:21616397-21616421	H1-hESC	embryonic stem cell:	n/a	chr4:21616398-21616409 chr4:21616398-21616409
50	MAFK	chr4:21594349-21594549	HepG2	liver:	n/a	chr4:21594432-21594443

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PACRGL-3	chr4:21583841-21583998	ENSG00000250092.2
2	lnc-PACRGL-3	chr4:21583719-21583748	ENSG00000250092.2
3	lnc-PACRGL-3	chr4:21610433-21610568	ENSG00000250092.2
4	lnc-PACRGL-3	chr4:21614955-21615351	ENSG00000250092.2

Variant related genes	Relation type
ENSG00000250092	TF binding region

Extended variants
information (count: 1262 )
Associated
traits (count: 59 )

Variant overlapped rSNPs/rCNVs (count:1262 , 50 per page) page: 1 2 3 4 5 6 7 ... 26

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs144188686	chr4:21580451-21580452	Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs564140455	chr4:21580511-21580512	Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs531182597	chr4:21580548-21580549	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs543412280	chr4:21580554-21580555	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs561780416	chr4:21580560-21580561	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs528957683	chr4:21580561-21580562	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs192053988	chr4:21580578-21580579	Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs73252260	chr4:21580673-21580674	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
9	rs533300694	chr4:21580676-21580677	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs551371887	chr4:21580684-21580685	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs376141233	chr4:21580702-21580703	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs537872743	chr4:21580707-21580708	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs73252261	chr4:21580727-21580728	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
14	rs184583010	chr4:21580738-21580739	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs28697050	chr4:21580791-21580792	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
16	rs188886402	chr4:21580886-21580887	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs560818895	chr4:21580917-21580918	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs373920977	chr4:21580924-21580925	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs367732973	chr4:21580944-21580945	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs56069015	chr4:21580986-21580987	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
21	rs558187675	chr4:21580994-21580995	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs116579684	chr4:21581054-21581055	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs193098037	chr4:21581104-21581105	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs543534255	chr4:21581152-21581153	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs7657068	chr4:21581191-21581192	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
26	rs573830847	chr4:21581194-21581195	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs111615442	chr4:21581212-21581213	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs184456066	chr4:21581264-21581265	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs140095883	chr4:21581277-21581278	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs532960876	chr4:21581348-21581349	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs552711706	chr4:21581382-21581383	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs112062758	chr4:21581383-21581384	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs7657482	chr4:21581417-21581418	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
34	rs372484527	chr4:21581431-21581432	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs530669079	chr4:21581433-21581434	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs78764828	chr4:21581443-21581444	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs568104230	chr4:21581473-21581474	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs189330150	chr4:21581477-21581478	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs547550040	chr4:21581511-21581512	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs77228359	chr4:21581518-21581519	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs181239522	chr4:21581519-21581520	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs558288498	chr4:21581553-21581554	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs576814180	chr4:21581590-21581591	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs537739931	chr4:21581599-21581600	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs144954596	chr4:21581615-21581616	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs16871492	chr4:21581652-21581653	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
47	rs541149885	chr4:21581669-21581670	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs59916546	chr4:21581698-21581699	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs559206011	chr4:21581725-21581726	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs577633584	chr4:21581726-21581727	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:59)

Disease	PMID	Source
Wilms tumour	21544195	CNVD
Breast cancer	17603634	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Colorectal cancer	19359472	CNVD
Neuroblastoma	17533364	CNVD
Oral squamous cell carcinoma	17134496	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Cancer	21637783	CNVD
Melanoma	21693616	CNVD
Squamous cell cancer	21044232	CNVD
Colorectal cancer	20709793	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Non-small cell lung cancer	21044232	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	17387387	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Cervical cancer	21062161	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Glioblastoma multiforme	21080181	CNVD
Chordoma	21602918	CNVD
HIV/AIDS	22032296	CNVD
Neuroblastoma	18923191	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Breast cancer	21785460	CNVD
Chronic lymphocytic leukemia	20421269	CNVD
Lung cancer	18438408	CNVD
Breast cancer	21858162	CNVD
small cell lung cancer	20016488	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Cancer	21183584	CNVD
Small bowel adenocarcinoma	21586687	CNVD
Gastric cancer	21586687	CNVD
Breast cancer	17133270	CNVD
lymphocytic leukemia	21291569	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	16608533	CNVD
Non-small cell lung cancer	21829676	CNVD
Melanoma	22183965	CNVD
Multiple myeloma	17550852	CNVD
Prostate cancer	18632612	CNVD
Olfactory neuroblastoma	18408657	CNVD
Burkitt''s lymphoma	20823134	CNVD
Burkitt''s lymphoma	19759907	CNVD
Myelofibrosis	22110671	CNVD
Colorectal cancer	16774939	CNVD
Pancreatic cancer	17952125	CNVD
Cancer	22183965	CNVD
Gastric cancer	16891809	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:21580200-21580600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr4:21580200-21580800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:21580600-21584400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr4:21580800-21582200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:21581200-21581600	Weak transcription	Fetal Heart	heart
6	chr4:21581600-21582800	Enhancers	Fetal Heart	heart
7	chr4:21582200-21582800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr4:21582800-21583800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr4:21583800-21584600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr4:21584400-21584600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr4:21590000-21590600	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr4:21590000-21590600	Enhancers	iPS-20b Cell Line	embryonic stem cell
13	chr4:21593400-21595200	Enhancers	Brain Hippocampus Middle	brain
14	chr4:21593600-21593800	Enhancers	Brain Inferior Temporal Lobe	brain
15	chr4:21593600-21594200	Enhancers	Brain Angular Gyrus	brain
16	chr4:21593800-21594200	Enhancers	Brain Cingulate Gyrus	brain
17	chr4:21593800-21597600	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr4:21594200-21597400	Weak transcription	Brain Angular Gyrus	brain
19	chr4:21594200-21598400	Weak transcription	Brain Cingulate Gyrus	brain
20	chr4:21594400-21594600	Enhancers	Brain Anterior Caudate	brain
21	chr4:21594600-21595600	Enhancers	Fetal Brain Male	brain
22	chr4:21594800-21595400	Enhancers	Ovary	ovary
23	chr4:21594800-21595600	Enhancers	Pancreatic Islets	Pancreatic Islet
24	chr4:21595000-21595800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr4:21595200-21595600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr4:21595200-21597400	Weak transcription	Brain Hippocampus Middle	brain
27	chr4:21597200-21597800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr4:21597200-21597800	Enhancers	Colon Smooth Muscle	Colon
29	chr4:21597200-21598000	Enhancers	HUES48 Cell Line	embryonic stem cell
30	chr4:21597200-21598000	Enhancers	HUES6 Cell Line	embryonic stem cell
31	chr4:21597200-21598800	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr4:21597400-21598200	Enhancers	Brain Hippocampus Middle	brain
33	chr4:21597400-21598600	Enhancers	Brain Anterior Caudate	brain
34	chr4:21597400-21598800	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr4:21597400-21599200	Enhancers	Brain Angular Gyrus	brain
36	chr4:21597600-21597800	Enhancers	Brain Inferior Temporal Lobe	brain
37	chr4:21597600-21598800	Enhancers	H9 Cell Line	embryonic stem cell
38	chr4:21597600-21598800	Enhancers	HUES64 Cell Line	embryonic stem cell
39	chr4:21597600-21599400	Enhancers	Brain Substantia Nigra	brain
40	chr4:21597800-21598200	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr4:21597800-21598800	Enhancers	iPS-18 Cell Line	embryonic stem cell
42	chr4:21598000-21598200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
43	chr4:21598000-21598200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
44	chr4:21598000-21598400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
45	chr4:21598000-21598600	Enhancers	Fetal Heart	heart
46	chr4:21598000-21598800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr4:21598000-21598800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
48	chr4:21598200-21598400	Enhancers	HUES48 Cell Line	embryonic stem cell
49	chr4:21598200-21598600	Active TSS	iPS-20b Cell Line	embryonic stem cell
50	chr4:21598200-21598600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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