Variant report

Variant	nsv516999
Chromosome Location	chr4:20548976-20565861
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:25)
CpG islands
(count:61)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:25 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr4:20561903-20562225	SK-N-SH_RA	brain:	n/a	n/a
2	EP300	chr4:20561888-20562289	SK-N-SH_RA	brain:	n/a	n/a
3	FOS	chr4:20555924-20556122	MCF10A-Er-Src	breast:	n/a	n/a
4	GATA3	chr4:20549615-20549643	SH-SY5Y	brain:	n/a	n/a
5	MAFF	chr4:20556056-20556344	HepG2	liver:	n/a	chr4:20556228-20556246
6	MAFK	chr4:20556071-20556369	HepG2	liver:	n/a	chr4:20556229-20556245 chr4:20556229-20556244
7	MAFK	chr4:20557773-20557955	H1-hESC	embryonic stem cell:	n/a	n/a
8	MAFK	chr4:20556104-20556382	IMR90	lung:	n/a	chr4:20556229-20556245 chr4:20556229-20556244
9	MAFK	chr4:20556077-20556400	HepG2	liver:	n/a	chr4:20556229-20556245 chr4:20556229-20556244
10	MYC	chr4:20555816-20556089	MCF10A-Er-Src	breast:	n/a	n/a
11	MYC	chr4:20555893-20556053	MCF10A-Er-Src	breast:	n/a	n/a
12	POLR2A	chr4:20560866-20560991	GM12878	blood:	n/a	n/a
13	POLR2A	chr4:20555888-20555992	MCF10A-Er-Src	breast:	n/a	n/a
14	POLR2A	chr4:20562018-20562068	MCF10A-Er-Src	breast:	n/a	n/a
15	POLR2A	chr4:20563227-20563287	MCF10A-Er-Src	breast:	n/a	n/a
16	POLR2A	chr4:20553841-20553975	ProgFib	skin:	n/a	n/a
17	POLR2A	chr4:20560202-20560267	MCF10A-Er-Src	breast:	n/a	n/a
18	POLR2A	chr4:20557692-20557719	MCF10A-Er-Src	breast:	n/a	n/a
19	POLR2A	chr4:20555840-20556040	MCF10A-Er-Src	breast:	n/a	n/a
20	POLR2A	chr4:20561333-20561503	MCF10A-Er-Src	breast:	n/a	n/a
21	STAT3	chr4:20550505-20550658	MCF10A-Er-Src	breast:	n/a	n/a
22	STAT3	chr4:20555269-20555280	MCF10A-Er-Src	breast:	n/a	n/a
23	STAT3	chr4:20554588-20554605	MCF10A-Er-Src	breast:	n/a	n/a
24	USF1	chr4:20563533-20563737	H1-hESC	embryonic stem cell:	n/a	n/a
25	ZNF143	chr4:20555870-20555994	H1-hESC	embryonic stem cell:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:20558003-20558053	IMR90	lung:	fetal
2	chr4:20558003-20558053	HCT-116	colon:	n/a
3	chr4:20558003-20558053	NB4	blood:	n/a
4	chr4:20558003-20558053	ovcar-3	ovarian:	n/a
5	chr4:20558003-20558053	BJ	skin:	n/a
6	chr4:20558003-20558053	Hepatocyte	liver:	n/a
7	chr4:20558003-20558053	HUVEC	blood vessel:	n/a
8	chr4:20558003-20558053	HEEpiC	esophagus:	n/a
9	chr4:20558003-20558053	Caco-2	colon:	n/a
10	chr4:20558003-20558053	SK-N-SH_RA	brain:	n/a
11	chr4:20558003-20558053	AG09309	skin:	n/a
12	chr4:20558003-20558053	GM12892	blood:	n/a
13	chr4:20558003-20558053	GM19239	blood:	n/a
14	chr4:20558003-20558053	SK-N-SH	brain:	n/a
15	chr4:20558003-20558053	NH-A	brain:	n/a
16	chr4:20558003-20558053	MCF10A-Er-Src	breast:	n/a
17	chr4:20558003-20558053	Jurkat	blood:	n/a
18	chr4:20558003-20558053	K562	blood:	n/a
19	chr4:20558003-20558053	HAEpiC	amniotic membrane:	n/a
20	chr4:20558003-20558053	HCPEpiC	choroid plexus:	n/a
21	chr4:20558003-20558053	HCF	heart:	n/a
22	chr4:20558003-20558053	HRE	kidney:	n/a
23	chr4:20558003-20558053	PANC-1	pancreas:	n/a
24	chr4:20558003-20558053	PrEC	prostate:	n/a
25	chr4:20558003-20558053	U87	brain:	n/a
26	chr4:20558003-20558053	NHBE	bronchial:	n/a
27	chr4:20558003-20558053	NHDF-neo	bronchial:	n/a
28	chr4:20558003-20558053	Hela-S3	cervix:	n/a
29	chr4:20558003-20558053	AoSMC	blood vessel:	n/a
30	chr4:20558003-20558053	AG04450	lung:	fetal
31	chr4:20558003-20558053	HRCEpiC	kidney:	n/a
32	chr4:20558003-20558053	HCM	heart:	n/a
33	chr4:20558003-20558053	HL-60	blood:	n/a
34	chr4:20558003-20558053	AG10803	skin:	n/a
35	chr4:20558003-20558053	PFSK-1	brain:	n/a
36	chr4:20558003-20558053	T-47D	breast:	n/a
37	chr4:20558003-20558053	GM12891	blood:	n/a
38	chr4:20558003-20558053	NT2-D1	testis:	n/a
39	chr4:20558003-20558053	HRPEpiC	eye:	n/a
40	chr4:20558003-20558053	HNPCEpiC	eye:	n/a
41	chr4:20558003-20558053	AG09319	gingival:	n/a
42	chr4:20558003-20558053	ECC-1	luminal epithelium:	n/a
43	chr4:20558003-20558053	LNCaP	prostate:	n/a
44	chr4:20558003-20558053	SKMC	muscle:	n/a
45	chr4:20558003-20558053	H1-hESC	embryonic stem cell:	embryo
46	chr4:20558003-20558053	BE2_C	brain:	n/a
47	chr4:20558003-20558053	CMK	blood:	n/a
48	chr4:20558003-20558053	MCF-7	breast:	n/a
49	chr4:20558003-20558053	SAEC	small airway:	n/a
50	chr4:20558003-20558053	A549	lung:	n/a

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:20423426..20426001-chr4:20546337..20549229,2	MCF-7	breast:
2	chr4:20555967..20557515-chr4:20560187..20562969,2	K562	blood:
3	chr4:20555229..20557515-chr4:20560187..20562423,2	K562	blood:
4	chr4:20555967..20557515-chr4:20560187..20562969,2	K562	blood:

No data

Variant related genes	Relation type
SLIT2	TF binding region
SLIT2	CpG island
ENSG00000145147	chromatin interactions

Extended variants
information (count: 662 )
Associated
traits (count: 60 )

Variant overlapped rSNPs/rCNVs (count:662 , 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	rs11936468	chr4:20548976-20548977	Weak transcription Strong transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs574264894	chr4:20548982-20548983	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs528936272	chr4:20548996-20548997	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs541594994	chr4:20549000-20549001	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs73252484	chr4:20549002-20549003	Weak transcription Strong transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
6	rs533466126	chr4:20549042-20549043	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs188318139	chr4:20549085-20549086	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs563783362	chr4:20549088-20549089	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs530881870	chr4:20549161-20549162	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs549422338	chr4:20549194-20549195	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs537798783	chr4:20549258-20549259	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs193175504	chr4:20549280-20549281	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs571482437	chr4:20549288-20549289	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs534011247	chr4:20549293-20549294	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs529207077	chr4:20549307-20549308	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs373226045	chr4:20549345-20549346	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs183698037	chr4:20549355-20549356	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs538658195	chr4:20549356-20549357	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs6847226	chr4:20549424-20549425	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
20	rs189092018	chr4:20549426-20549427	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs551013003	chr4:20549479-20549480	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs569432378	chr4:20549481-20549482	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs536613222	chr4:20549544-20549545	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs78727484	chr4:20549640-20549641	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs574249716	chr4:20549654-20549655	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs535056906	chr4:20549669-20549670	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs143537081	chr4:20549683-20549684	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs578082184	chr4:20549694-20549695	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs545621987	chr4:20549701-20549702	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs563745844	chr4:20549719-20549720	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs575824115	chr4:20549737-20549738	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs543027546	chr4:20549750-20549751	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs151250524	chr4:20549788-20549789	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs140479905	chr4:20549793-20549794	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs547332789	chr4:20549795-20549796	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs150015533	chr4:20549832-20549833	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs556654768	chr4:20549862-20549863	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs532953197	chr4:20549867-20549868	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs551174416	chr4:20549872-20549873	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs191238353	chr4:20549882-20549883	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs536774023	chr4:20549900-20549901	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs548569966	chr4:20549903-20549904	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs41266539	chr4:20549927-20549928	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs576076486	chr4:20549952-20549953	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs553344706	chr4:20549968-20549969	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs578213760	chr4:20549969-20549970	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs369179668	chr4:20550052-20550053	Weak transcription Genic enhancers Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs557622213	chr4:20550068-20550069	Weak transcription Genic enhancers Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs375099406	chr4:20550138-20550139	Weak transcription Genic enhancers Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs138378764	chr4:20550143-20550144	Weak transcription Genic enhancers Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:60)

Disease	PMID	Source
Oral squamous cell carcinoma	17134496	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
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
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
Breast cancer	16608533	CNVD
Non-small cell lung cancer	21829676	CNVD
Melanoma	22183965	CNVD
Multiple myeloma	17550852	CNVD
Prostate cancer	18632612	CNVD
Ovarian cancer	17908972	CNVD
Olfactory neuroblastoma	18408657	CNVD
Burkitt''s lymphoma	20823134	CNVD
Burkitt''s lymphoma	19759907	CNVD
Myelofibrosis	22110671	CNVD
Colorectal cancer	16774939	CNVD
Breast cancer	22522925	CNVD
Breast cancer	22737080	CNVD
Lung squamous cell carcinoma	22363434	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:20492000-20599800	Weak transcription	Aorta	Aorta
2	chr4:20511800-20576200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr4:20519400-20571000	Weak transcription	Adipose Nuclei	Adipose
4	chr4:20524200-20555200	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr4:20525200-20555400	Weak transcription	Stomach Smooth Muscle	stomach
6	chr4:20530400-20555400	Weak transcription	NHEK	skin
7	chr4:20533000-20578000	Weak transcription	NHLF	lung
8	chr4:20533800-20576200	Weak transcription	Left Ventricle	heart
9	chr4:20534600-20552800	Weak transcription	Brain Anterior Caudate	brain
10	chr4:20534800-20576400	Weak transcription	Fetal Brain Male	brain
11	chr4:20535800-20593600	Weak transcription	Fetal Kidney	kidney
12	chr4:20536000-20552400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr4:20536000-20554800	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr4:20536000-20555200	Weak transcription	Fetal Muscle Trunk	muscle
15	chr4:20536600-20572200	Weak transcription	Placenta	Placenta
16	chr4:20536800-20618600	Weak transcription	Spleen	Spleen
17	chr4:20537800-20552600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr4:20537800-20552600	Weak transcription	Colon Smooth Muscle	Colon
19	chr4:20537800-20552800	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr4:20538000-20553200	Weak transcription	Fetal Stomach	stomach
21	chr4:20539000-20552800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr4:20541200-20552800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr4:20543600-20549600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr4:20543600-20549800	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr4:20545000-20549800	Weak transcription	Osteobl	bone
26	chr4:20545000-20552600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr4:20546800-20550000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr4:20546800-20550600	Strong transcription	Fetal Lung	lung
29	chr4:20547000-20576000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr4:20547400-20550800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr4:20547800-20549800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr4:20548000-20550000	Weak transcription	NHDF-Ad	bronchial
33	chr4:20548600-20549200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr4:20548800-20549200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr4:20549200-20568800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr4:20549600-20550600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr4:20549800-20550600	Strong transcription	Placenta Amnion	Placenta Amnion
38	chr4:20549800-20550600	Strong transcription	Osteobl	bone
39	chr4:20549800-20550800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr4:20550000-20550400	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr4:20550000-20561400	Strong transcription	NHDF-Ad	bronchial
42	chr4:20550400-20561000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr4:20550600-20552000	Weak transcription	Fetal Lung	lung
44	chr4:20550600-20552400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr4:20550600-20552400	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr4:20550600-20552400	Weak transcription	Osteobl	bone
47	chr4:20550800-20552600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr4:20550800-20553400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr4:20552000-20554800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr4:20552000-20557600	Strong transcription	Fetal Lung	lung

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