Variant report

Variant	esv3468239
Chromosome Location	chr4:55805112-55807129
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	GATA3	chr4:55806720-55806982	MCF-7	breast:	n/a	n/a
2	GATA3	chr4:55806715-55806969	T-47D	breast:	n/a	n/a
3	POLR2A	chr4:55805954-55806016	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
ENSG00000248317	TF binding region

Extended variants
information (count: 88 )
Associated
traits (count: 92 )

Variant overlapped rSNPs/rCNVs (count:88 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs147510061	chr4:55805123-55805124	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs35908949	chr4:55805136-55805137	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs79894118	chr4:55805174-55805175	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs543853986	chr4:55805180-55805181	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs59049699	chr4:55805199-55805200	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
6	rs140223681	chr4:55805210-55805211	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs556702619	chr4:55805230-55805231	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs548721314	chr4:55805242-55805243	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs6855577	chr4:55805256-55805257	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
10	rs6855603	chr4:55805287-55805288	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs553241325	chr4:55805293-55805294	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs573095925	chr4:55805295-55805296	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs116105461	chr4:55805322-55805323	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs372404805	chr4:55805323-55805324	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs552882813	chr4:55805374-55805375	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs145647214	chr4:55805375-55805376	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs578119884	chr4:55805386-55805387	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs6838962	chr4:55805391-55805392	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
19	rs563826424	chr4:55805412-55805413	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs113929754	chr4:55805413-55805414	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs529520615	chr4:55805435-55805436	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs549355402	chr4:55805442-55805443	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs145389415	chr4:55805445-55805446	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs528812877	chr4:55805506-55805507	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs551343827	chr4:55805507-55805508	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs202110169	chr4:55805534-55805535	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs76701687	chr4:55805542-55805543	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs74841164	chr4:55805543-55805544	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs2067951	chr4:55805555-55805556	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
30	rs530492884	chr4:55805556-55805557	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs550262054	chr4:55805601-55805602	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs2067950	chr4:55805654-55805655	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
33	rs114841648	chr4:55805712-55805713	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs568108723	chr4:55805733-55805734	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs76423490	chr4:55805748-55805749	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs148723198	chr4:55805782-55805783	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs142248275	chr4:55805794-55805795	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs113787632	chr4:55805802-55805803	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs191706738	chr4:55805803-55805804	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs543897440	chr4:55805830-55805831	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs183604701	chr4:55805851-55805852	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs574234415	chr4:55805983-55805984	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
43	rs188957114	chr4:55805986-55805987	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
44	rs193255721	chr4:55806007-55806008	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
45	rs112498805	chr4:55806008-55806009	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
46	rs145502869	chr4:55806075-55806076	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs529469910	chr4:55806129-55806130	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs564491252	chr4:55806134-55806135	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs183672274	chr4:55806143-55806144	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs186710214	chr4:55806169-55806170	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:92)

Disease	PMID	Source
Gastrointestinal stromal cancer	16982739	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Glioblastoma multiforme	21080181	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Chordoma	21602918	CNVD
HIV/AIDS	22032296	CNVD
Medulloblastoma	21979893	CNVD
Neuroblastoma	18923191	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Autism	22495311	CNVD
Breast cancer	21858162	CNVD
Small bowel adenocarcinoma	21586687	CNVD
Gastric cancer	21586687	CNVD
lymphocytic leukemia	21291569	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Non-small cell lung cancer	21829676	CNVD
Melanoma	22183965	CNVD
Melanoma	18172304	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Lung cancer	18438408	CNVD
Renal cell carcinoma	18194544	CNVD
Breast cancer	17603634	CNVD
Glioblastoma multiforme	21922591	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Parkinson disease	21956041	CNVD
Mental retardation	20522426	CNVD
delayed speech	20522426	CNVD
growth disorder	20522426	CNVD
Hepatocellular carcinoma	16750200	CNVD
Myxofibrosarcoma	16751306	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Acute myeloid leukemia	20729466	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Parkinson disease	18923514	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Cancer	21183584	CNVD
Breast cancer	16272173	CNVD
Glioblastoma multiforme	19435819	CNVD
Multiple myeloma	16616336	CNVD
Colorectal cancer	19359472	CNVD
Malignant mesothelioma	18160781	CNVD
Medulloblastoma	18056178	CNVD
Multiple myeloma	17077331	CNVD
Pleural malignant mesothelioma	18160781	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
4q-syndrome	17576883	CNVD
Cancer	21637783	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Colorectal cancer	20709793	CNVD
Muscular dystrophy	21149563	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	17387387	CNVD
Hepatocellular carcinoma	22174799	CNVD
Liposarcoma	21253554	CNVD
Oligodendroglial tumors	17285580	CNVD
Cervical cancer	21062161	CNVD
Myelofibrosis	22110671	CNVD
Glioblastoma multiforme	22286061	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Ovarian neoplasms	16753589	CNVD
Metanephric adenoma	20802469	CNVD
Breast cancer	16608533	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Glioblastoma multiforme	21569311	CNVD
Glioblastoma	17504929	CNVD
Glioblastoma	16823502	CNVD
Melanoma	16908931	CNVD
Glioblastoma	20031968	CNVD
Medulloblastoma	19270706	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Olfactory neuroblastoma	18408657	CNVD
Basal cell lymphoma	19029149	CNVD
Diffuse large b-cell lymphoma	19029149	CNVD
Esophageal squamous carcinoma	17470683	CNVD
Rhabdomyosarcoma	16790082	CNVD
Gastrointestinal stromal cancer	17438095	CNVD
Colorectal cancer	16272173	CNVD
Lung cancer	19208797	CNVD
small cell lung cancer	20016488	CNVD
Glioblastoma multiforme	19115005	CNVD
Wilms tumour	21544195	CNVD
Glioblastoma multiforme	21138945	CNVD
Cancer	20164920	CNVD
Cancer	22183965	CNVD
Autism	22543975	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:55796800-55810200	Weak transcription	Fetal Muscle Leg	muscle
2	chr4:55802600-55807600	Weak transcription	Fetal Stomach	stomach
3	chr4:55802600-55808200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:55803200-55806800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr4:55803400-55806800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr4:55804000-55805800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr4:55804000-55808200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr4:55804200-55806800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr4:55804200-55808800	Weak transcription	Stomach Mucosa	stomach
10	chr4:55804200-55811200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr4:55804400-55805800	Weak transcription	HUVEC	blood vessel
12	chr4:55804400-55808000	Weak transcription	NH-A	brain
13	chr4:55804600-55805600	Weak transcription	Primary hematopoietic stem cells	blood
14	chr4:55804800-55805800	Weak transcription	Primary T cells from cord blood	blood
15	chr4:55805000-55806000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr4:55805600-55807600	Enhancers	Primary hematopoietic stem cells	blood
17	chr4:55805800-55806800	Enhancers	Primary T cells from cord blood	blood
18	chr4:55805800-55806800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr4:55805800-55807600	Enhancers	HUVEC	blood vessel
20	chr4:55806000-55807400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr4:55806000-55809600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr4:55806000-55809800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr4:55806200-55807200	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr4:55806200-55808000	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr4:55806200-55810000	Enhancers	Primary T cells fromperipheralblood	blood
26	chr4:55806400-55806800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr4:55806400-55808000	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr4:55806400-55808000	Enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr4:55806400-55808600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr4:55806400-55809600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr4:55806800-55807000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr4:55806800-55807200	Enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr4:55806800-55807200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
34	chr4:55806800-55807800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr4:55806800-55808200	Enhancers	Fetal Lung	lung
36	chr4:55806800-55808400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
37	chr4:55806800-55808400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
38	chr4:55806800-55808600	Flanking Active TSS	Primary T cells from cord blood	blood
39	chr4:55806800-55808600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr4:55806800-55809000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr4:55806800-55809200	Enhancers	Thymus	Thymus
42	chr4:55806800-55809600	Enhancers	Primary B cells from peripheral blood	blood
43	chr4:55806800-55812600	Enhancers	Fetal Thymus	thymus
44	chr4:55807000-55807600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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