Variant report

Variant	esv3366988
Chromosome Location	chr4:55808045-55809893
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	CTCF	chr4:55808000-55808150	HUVEC	blood vessel:	n/a	n/a
2	FOS	chr4:55807984-55808705	HUVEC	blood vessel:	n/a	n/a
3	GATA2	chr4:55808052-55809135	HUVEC	blood vessel:	n/a	chr4:55808649-55808656 chr4:55808649-55808656 chr4:55808649-55808656 chr4:55808313-55808323 chr4:55808421-55808431
4	JUN	chr4:55807674-55809099	HUVEC	blood vessel:	n/a	chr4:55808972-55808979 chr4:55808967-55808978 chr4:55808971-55808979
5	POLR2A	chr4:55807948-55808699	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr4:55807925-55808651	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr4:55808168-55808658	HUVEC	blood vessel:	n/a	n/a
8	POLR2A	chr4:55809267-55809416	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr4:55807986-55808595	HUVEC	blood vessel:	n/a	n/a
10	POLR2A	chr4:55808296-55808463	HUVEC	blood vessel:	n/a	n/a
11	SPI1	chr4:55808961-55809273	HL-60	blood:	n/a	chr4:55809086-55809093 chr4:55809115-55809122
12	TBL1XR1	chr4:55809048-55809128	GM12878	blood:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KIT-2	chr4:55809796-55809853	XLOC_003542

Variant related genes	Relation type
ENSG00000248317	TF binding region

Extended variants
information (count: 68 )
Associated
traits (count: 92 )

Variant overlapped rSNPs/rCNVs (count:68 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs73143600	chr4:55808047-55808048	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs188372461	chr4:55808058-55808059	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
3	rs575124567	chr4:55808095-55808096	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
4	rs367688104	chr4:55808153-55808154	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
5	rs139944621	chr4:55808248-55808249	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region	1 gene(s)	Overlapped CNVs	n/a
6	rs180786950	chr4:55808283-55808284	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region	1 gene(s)	Overlapped CNVs	n/a
7	rs371109381	chr4:55808306-55808307	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region	1 gene(s)	Overlapped CNVs	n/a
8	rs371762346	chr4:55808354-55808355	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region	1 gene(s)	Overlapped CNVs	n/a
9	rs542343259	chr4:55808364-55808365	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region	1 gene(s)	Overlapped CNVs	n/a
10	rs116229337	chr4:55808371-55808372	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region	1 gene(s)	Overlapped CNVs	n/a
11	rs149782610	chr4:55808377-55808378	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region	1 gene(s)	Overlapped CNVs	n/a
12	rs566561926	chr4:55808382-55808383	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region	1 gene(s)	Overlapped CNVs	n/a
13	rs144676852	chr4:55808396-55808397	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region	1 gene(s)	Overlapped CNVs	n/a
14	rs8180203	chr4:55808418-55808419	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
15	rs546378775	chr4:55808506-55808507	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
16	rs542084932	chr4:55808549-55808550	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
17	rs79765631	chr4:55808551-55808552	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
18	rs527611349	chr4:55808608-55808609	Weak transcription Active TSS Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
19	rs6829950	chr4:55808625-55808626	Weak transcription Active TSS Enhancers	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
20	rs566874182	chr4:55808654-55808655	Weak transcription Active TSS Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
21	rs532441537	chr4:55808659-55808660	Weak transcription Active TSS Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
22	rs6829974	chr4:55808660-55808661	Weak transcription Active TSS Enhancers	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
23	rs373327226	chr4:55808683-55808684	Weak transcription Active TSS Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
24	rs200926592	chr4:55808686-55808687	Weak transcription Active TSS Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
25	rs201756413	chr4:55808687-55808688	Weak transcription Active TSS Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
26	rs199926900	chr4:55808688-55808689	Weak transcription Active TSS Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
27	rs555174643	chr4:55808697-55808698	Weak transcription Active TSS Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
28	rs576600915	chr4:55808729-55808730	Weak transcription Active TSS Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
29	rs79016546	chr4:55808913-55808914	Weak transcription Active TSS Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
30	rs373453313	chr4:55808918-55808919	Weak transcription Active TSS Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
31	rs534524986	chr4:55809027-55809028	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
32	rs12639867	chr4:55809040-55809041	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
33	rs551827764	chr4:55809068-55809069	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
34	rs576913719	chr4:55809119-55809120	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
35	rs3893245	chr4:55809222-55809223	Weak transcription Enhancers Flanking Active TSS	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
36	rs528875301	chr4:55809259-55809260	Weak transcription Enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
37	rs12639878	chr4:55809301-55809302	Weak transcription Enhancers Flanking Active TSS	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
38	rs576249639	chr4:55809303-55809304	Weak transcription Enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
39	rs565386831	chr4:55809336-55809337	Weak transcription Enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
40	rs80109596	chr4:55809343-55809344	Weak transcription Enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
41	rs561952590	chr4:55809360-55809361	Weak transcription Enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
42	rs527555957	chr4:55809361-55809362	Weak transcription Enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
43	rs541339257	chr4:55809375-55809376	Weak transcription Enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
44	rs560240462	chr4:55809449-55809450	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
45	rs532363253	chr4:55809504-55809505	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
46	rs368692830	chr4:55809514-55809515	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
47	rs552202142	chr4:55809553-55809554	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
48	rs547381143	chr4:55809556-55809557	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
49	rs144274522	chr4:55809566-55809567	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
50	rs76278120	chr4:55809569-55809570	Weak transcription Enhancers Flanking Active TSS	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:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:55796800-55810200	Weak transcription	Fetal Muscle Leg	muscle
2	chr4:55802600-55808200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:55804000-55808200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr4:55804200-55808800	Weak transcription	Stomach Mucosa	stomach
5	chr4:55804200-55811200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr4:55806000-55809600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
7	chr4:55806000-55809800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr4:55806200-55810000	Enhancers	Primary T cells fromperipheralblood	blood
9	chr4:55806400-55808600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr4:55806400-55809600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr4:55806800-55808200	Enhancers	Fetal Lung	lung
12	chr4:55806800-55808400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
13	chr4:55806800-55808400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
14	chr4:55806800-55808600	Flanking Active TSS	Primary T cells from cord blood	blood
15	chr4:55806800-55808600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr4:55806800-55809000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr4:55806800-55809200	Enhancers	Thymus	Thymus
18	chr4:55806800-55809600	Enhancers	Primary B cells from peripheral blood	blood
19	chr4:55806800-55812600	Enhancers	Fetal Thymus	thymus
20	chr4:55807200-55808400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
21	chr4:55807200-55810400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr4:55807400-55808200	Enhancers	Fetal Brain Female	brain
23	chr4:55807400-55808400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr4:55807400-55809000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
25	chr4:55807600-55808200	Active TSS	Duodenum Mucosa	Duodenum
26	chr4:55807600-55808200	Flanking Active TSS	HUVEC	blood vessel
27	chr4:55807600-55808600	Flanking Active TSS	Primary B cells from cord blood	blood
28	chr4:55807600-55808600	Flanking Active TSS	Primary hematopoietic stem cells	blood
29	chr4:55807600-55809000	Active TSS	Monocytes-CD14+_RO01746	blood
30	chr4:55807600-55809200	Enhancers	Brain Inferior Temporal Lobe	brain
31	chr4:55807600-55809200	Enhancers	Fetal Stomach	stomach
32	chr4:55807800-55808200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
33	chr4:55807800-55808200	Enhancers	Brain Cingulate Gyrus	brain
34	chr4:55807800-55808200	Flanking Active TSS	Brain Substantia Nigra	brain
35	chr4:55807800-55808200	Active TSS	Stomach Smooth Muscle	stomach
36	chr4:55807800-55808400	Enhancers	Adipose Nuclei	Adipose
37	chr4:55807800-55808400	Active TSS	Colonic Mucosa	Colon
38	chr4:55807800-55809200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
39	chr4:55808000-55808200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
40	chr4:55808000-55808200	Bivalent/Poised TSS	Brain Angular Gyrus	brain
41	chr4:55808000-55808200	Enhancers	Brain Hippocampus Middle	brain
42	chr4:55808000-55808400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr4:55808000-55808400	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr4:55808000-55808400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
45	chr4:55808000-55808400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr4:55808000-55808400	Active TSS	Brain Anterior Caudate	brain
47	chr4:55808000-55808400	Enhancers	NH-A	brain
48	chr4:55808000-55808600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
49	chr4:55808000-55808600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
50	chr4:55808000-55808600	Enhancers	Fetal Kidney	kidney

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