Variant report

Variant	nsv979765
Chromosome Location	chr3:28401267-28427998
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	BRCA1	chr3:28402154-28402199	H1-hESC	embryonic stem cell:	n/a	n/a
2	CEBPB	chr3:28417900-28418424	Hela-S3	cervix:	n/a	chr3:28418116-28418127 chr3:28418264-28418277
3	CEBPB	chr3:28417987-28418380	A549	lung:	n/a	chr3:28418116-28418127 chr3:28418264-28418277
4	CEBPB	chr3:28417857-28418399	IMR90	lung:	n/a	chr3:28418116-28418127 chr3:28418264-28418277
5	CEBPB	chr3:28417961-28418396	HepG2	liver:	n/a	chr3:28418116-28418127 chr3:28418264-28418277
6	CTCF	chr3:28413220-28413370	GM12864	blood:	n/a	n/a
7	E2F4	chr3:28417807-28418469	MCF10A-Er-Src	breast:	n/a	n/a
8	EP300	chr3:28417977-28418357	Hela-S3	cervix:	n/a	chr3:28418262-28418276
9	FOS	chr3:28417821-28418361	MCF10A-Er-Src	breast:	n/a	n/a
10	FOS	chr3:28417853-28418383	MCF10A-Er-Src	breast:	n/a	n/a
11	FOS	chr3:28417859-28418409	MCF10A-Er-Src	breast:	n/a	n/a
12	FOS	chr3:28417821-28418398	MCF10A-Er-Src	breast:	n/a	n/a
13	FOXA2	chr3:28411011-28411640	A549	lung:	n/a	n/a
14	MAX	chr3:28427602-28427931	NB4	blood:	n/a	n/a
15	MYC	chr3:28417869-28418351	MCF10A-Er-Src	breast:	n/a	n/a
16	MYC	chr3:28417858-28418398	MCF10A-Er-Src	breast:	n/a	n/a
17	MYC	chr3:28427654-28427857	NB4	blood:	n/a	n/a
18	POLR2A	chr3:28417914-28418296	U87	brain:	n/a	n/a
19	POLR2A	chr3:28403025-28403134	MCF10A-Er-Src	breast:	n/a	n/a
20	POLR2A	chr3:28403370-28403496	MCF10A-Er-Src	breast:	n/a	n/a
21	POLR2A	chr3:28417900-28418296	U87	brain:	n/a	n/a
22	POLR2A	chr3:28417791-28418366	MCF10A-Er-Src	breast:	n/a	n/a
23	POLR2A	chr3:28403808-28404214	MCF10A-Er-Src	breast:	n/a	n/a
24	POLR2A	chr3:28424850-28424857	MCF10A-Er-Src	breast:	n/a	n/a
25	POLR2A	chr3:28402661-28402766	MCF10A-Er-Src	breast:	n/a	n/a
26	POLR2A	chr3:28401309-28401458	MCF10A-Er-Src	breast:	n/a	n/a
27	POLR2A	chr3:28423440-28423525	HepG2	liver:	n/a	n/a
28	POLR2A	chr3:28402330-28402357	MCF10A-Er-Src	breast:	n/a	n/a
29	POLR2A	chr3:28404311-28404406	GM12878	blood:	n/a	n/a
30	POLR2A	chr3:28403817-28403832	MCF10A-Er-Src	breast:	n/a	n/a
31	POLR2A	chr3:28417881-28418397	MCF10A-Er-Src	breast:	n/a	n/a
32	REST	chr3:28409284-28409425	H1-hESC	embryonic stem cell:	n/a	n/a
33	SP1	chr3:28409265-28409451	HepG2	liver:	n/a	n/a
34	SPI1	chr3:28427619-28427832	GM12878	blood:	n/a	n/a
35	SPI1	chr3:28427559-28427876	GM12891	blood:	n/a	n/a
36	SPI1	chr3:28427558-28427846	K562	blood:	n/a	n/a
37	SPI1	chr3:28427569-28427869	GM12878	blood:	n/a	n/a
38	SPI1	chr3:28407375-28407775	GM12878	blood:	n/a	n/a
39	SPI1	chr3:28427459-28427972	GM12878	blood:	n/a	n/a
40	SPI1	chr3:28427554-28427864	GM12891	blood:	n/a	n/a
41	SPI1	chr3:28427482-28427967	HL-60	blood:	n/a	n/a
42	SPI1	chr3:28427533-28427965	HL-60	blood:	n/a	n/a
43	SPI1	chr3:28427584-28427859	K562	blood:	n/a	n/a
44	STAT3	chr3:28417764-28418350	MCF10A-Er-Src	breast:	n/a	n/a
45	STAT3	chr3:28416689-28416835	MCF10A-Er-Src	breast:	n/a	n/a
46	STAT3	chr3:28417821-28418386	MCF10A-Er-Src	breast:	n/a	n/a
47	STAT3	chr3:28417974-28418308	Hela-S3	cervix:	n/a	n/a
48	STAT3	chr3:28417821-28418437	MCF10A-Er-Src	breast:	n/a	n/a
49	ZBTB33	chr3:28409269-28409447	HepG2	liver:	n/a	n/a
50	ZNF274	chr3:28423036-28423260	NT2-D1	testis:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:28390221..28392095-chr3:28400172..28402112,2	K562	blood:
2	chr3:28391232..28393248-chr3:28418194..28419782,2	K562	blood:
3	chr3:28389727..28391641-chr3:28410342..28411907,2	K562	blood:
4	chr3:28388460..28394013-chr3:28397646..28403545,9	K562	blood:

Variant related genes	Relation type
ZCWPW2	TF binding region
ENSG00000163512	chromatin interactions
ENSG00000206559	chromatin interactions

Extended variants
information (count: 851 )
Associated
traits (count: 74 )

Variant overlapped rSNPs/rCNVs (count:851 , 50 per page) page: 1 2 3 4 5 6 7 ... 18

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs535948359	chr3:28401324-28401325	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
2	rs139035536	chr3:28401379-28401380	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs141539385	chr3:28401415-28401416	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
4	rs56315087	chr3:28401454-28401455	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
5	rs544865096	chr3:28401465-28401466	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
6	rs566568893	chr3:28401500-28401501	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
7	rs558360018	chr3:28401521-28401522	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
8	rs143839185	chr3:28401579-28401580	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
9	rs540535377	chr3:28401587-28401588	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
10	rs148162536	chr3:28401590-28401591	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
11	rs529142643	chr3:28401610-28401611	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs528833430	chr3:28401617-28401618	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
13	rs542715450	chr3:28401629-28401630	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
14	rs562482281	chr3:28401652-28401653	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
15	rs141960863	chr3:28401688-28401689	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
16	rs150672713	chr3:28401723-28401724	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
17	rs571078122	chr3:28401724-28401725	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
18	rs527605054	chr3:28401735-28401736	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
19	rs569971794	chr3:28401797-28401798	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
20	rs547328613	chr3:28401812-28401813	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
21	rs372986373	chr3:28401838-28401839	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
22	rs376682732	chr3:28401841-28401842	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
23	rs78752882	chr3:28401862-28401863	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
24	rs71087692	chr3:28401864-28401865	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
25	rs77613591	chr3:28401866-28401867	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
26	rs138932233	chr3:28401882-28401883	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
27	rs13090951	chr3:28401883-28401884	Weak transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
28	rs13070434	chr3:28401896-28401897	Weak transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
29	rs61620434	chr3:28401924-28401925	Weak transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
30	rs112507128	chr3:28401945-28401946	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
31	rs538326054	chr3:28401963-28401964	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
32	rs544341658	chr3:28401982-28401983	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
33	rs558398803	chr3:28401999-28402000	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
34	rs537775124	chr3:28402003-28402004	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
35	rs372757609	chr3:28402013-28402014	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
36	rs201957654	chr3:28402014-28402015	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
37	rs551621698	chr3:28402046-28402047	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
38	rs554126524	chr3:28402051-28402052	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
39	rs182067302	chr3:28402057-28402058	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
40	rs542288382	chr3:28402121-28402122	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
41	rs117691885	chr3:28402131-28402132	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
42	rs531324312	chr3:28402146-28402147	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
43	rs115580393	chr3:28402204-28402205	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
44	rs570769895	chr3:28402221-28402222	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
45	rs564741266	chr3:28402224-28402225	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
46	rs370185344	chr3:28402228-28402229	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
47	rs187042194	chr3:28402286-28402287	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
48	rs13095675	chr3:28402320-28402321	Weak transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
49	rs529978410	chr3:28402359-28402360	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
50	rs549142928	chr3:28402370-28402371	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:74)

Disease	PMID	Source
Chronic lymphocytic leukemia	21546498	CNVD
Breast cancer	17603634	CNVD
Neuroblastoma	17327916	CNVD
Glioblastoma multiforme	21080181	CNVD
Neuroblastoma	18923191	CNVD
Colorectal cancer	21297112	CNVD
Lynch syndrome	18415027	CNVD
Renal cell carcinoma	18592004	CNVD
Acute myeloid leukemia	20729466	CNVD
Urothelial carcinoma	18382360	CNVD
Melanoma	18172304	CNVD
Cervical cancer	21062161	CNVD
Hirschsprung''s Disease	21712996	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
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
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Retinoblastoma	21504564	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
lymphocytic leukemia	21291569	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Renal cell carcinoma	21668985	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Lung cancer	20668451	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Intellectual disability	22102821	CNVD
Esophageal cancer	20955586	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Squamous cell cancer	20885788	CNVD
Breast cancer	17133270	CNVD
Uveal melanoma	20484589	CNVD
Autism	22495311	CNVD
Melanoma	20688739	CNVD
Acute myeloid leukemia	21251322	CNVD
Myelofibrosis	22110671	CNVD
Lung cancer	16618734	CNVD
Cancer	20164919	CNVD
Developmental delay	21147756	CNVD
Schizophrenia	18511947	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:28393800-28412200	Weak transcription	Pancreas	Pancrea
2	chr3:28412200-28412400	Enhancers	Pancreas	Pancrea
3	chr3:28413200-28413600	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr3:28417400-28417600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr3:28417400-28417800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr3:28417600-28417800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr3:28417600-28418000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr3:28417800-28418000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr3:28417800-28418400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr3:28417800-28418400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr3:28417800-28418400	Enhancers	Osteobl	bone
12	chr3:28418000-28418400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr3:28418000-28418400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr3:28418000-28418600	Active TSS	Monocytes-CD14+_RO01746	blood
15	chr3:28418000-28418800	Active TSS	Fetal Lung	lung
16	chr3:28418200-28418600	Active TSS	Adipose Nuclei	Adipose
17	chr3:28418200-28419000	Enhancers	Hela-S3	cervix
18	chr3:28418400-28418800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr3:28418400-28418800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr3:28418400-28419000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr3:28418400-28419200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr3:28418600-28418800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
23	chr3:28418800-28419000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr3:28418800-28419000	Enhancers	Monocytes-CD14+_RO01746	blood
25	chr3:28419200-28419600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr3:28420800-28433000	Weak transcription	Ovary	ovary
27	chr3:28425200-28431400	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr3:28426000-28433000	Weak transcription	Right Ventricle	heart

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