Variant report

Variant	esv3365493
Chromosome Location	chr2:55677866-55682407
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	PAX5	chr2:55680086-55680503	GM12878	blood:	n/a	chr2:55680274-55680283 chr2:55680274-55680292 chr2:55680273-55680290 chr2:55680273-55680292
2	PAX5	chr2:55680107-55680553	GM12892	blood:	n/a	chr2:55680274-55680283 chr2:55680274-55680292 chr2:55680273-55680290 chr2:55680273-55680292
3	PAX5	chr2:55680141-55680436	GM12892	blood:	n/a	chr2:55680274-55680283 chr2:55680274-55680292 chr2:55680273-55680290 chr2:55680273-55680292
4	PAX5	chr2:55680009-55680561	GM12878	blood:	n/a	chr2:55680274-55680283 chr2:55680274-55680292 chr2:55680273-55680290 chr2:55680273-55680292
5	PAX5	chr2:55680080-55680465	GM12878	blood:	n/a	chr2:55680274-55680283 chr2:55680274-55680292 chr2:55680273-55680290 chr2:55680273-55680292
6	PAX5	chr2:55680019-55680509	GM12891	blood:	n/a	chr2:55680274-55680283 chr2:55680274-55680292 chr2:55680273-55680290 chr2:55680273-55680292
7	PAX5	chr2:55680143-55680392	GM12878	blood:	n/a	chr2:55680274-55680283 chr2:55680274-55680292 chr2:55680273-55680290 chr2:55680273-55680292
8	STAT3	chr2:55680643-55680693	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55461063..55464036-chr2:55678930..55681673,2	MCF-7	breast:
2	chr2:55676747..55678415-chr2:55678423..55681362,2	K562	blood:

Variant related genes	Relation type
RNU6-775P	TF binding region
ENSG00000238619	chromatin interactions

Extended variants
information (count: 203 )
Associated
traits (count: 80 )

Variant overlapped rSNPs/rCNVs (count:203 , 50 per page) page: 1 2 3 4 5

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs111537847	chr2:55678430-55678431	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
2	rs570040824	chr2:55678477-55678478	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs191696126	chr2:55678478-55678479	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
4	rs552800504	chr2:55678492-55678493	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs565548813	chr2:55678519-55678520	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
6	rs534560605	chr2:55678527-55678528	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs554749664	chr2:55678558-55678559	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs184480796	chr2:55678585-55678586	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs187938337	chr2:55678602-55678603	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs6736128	chr2:55678604-55678605	Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs557216581	chr2:55678639-55678640	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs6751355	chr2:55678675-55678676	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs6736247	chr2:55678694-55678695	Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
14	rs370169670	chr2:55678695-55678696	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs553186013	chr2:55678711-55678712	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs572397028	chr2:55678782-55678783	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs75108578	chr2:55678814-55678815	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs547068975	chr2:55678827-55678828	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs112535895	chr2:55678868-55678869	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs530110893	chr2:55678888-55678889	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs543481391	chr2:55678910-55678911	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
22	rs566993329	chr2:55678920-55678921	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs372547681	chr2:55678936-55678937	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
24	rs147391501	chr2:55678947-55678948	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
25	rs552594951	chr2:55678987-55678988	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs566357127	chr2:55679006-55679007	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs377422230	chr2:55679101-55679102	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
28	rs559003506	chr2:55679103-55679104	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs375608017	chr2:55679122-55679123	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
30	rs113989151	chr2:55679137-55679138	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
31	rs139538989	chr2:55679152-55679153	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs568034930	chr2:55679155-55679156	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
33	rs537161185	chr2:55679182-55679183	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs550658464	chr2:55679184-55679185	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs570560547	chr2:55679185-55679186	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs539617129	chr2:55679213-55679214	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs553033734	chr2:55679225-55679226	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
38	rs111885668	chr2:55679231-55679232	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
39	rs572350118	chr2:55679258-55679259	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
40	rs192219072	chr2:55679284-55679285	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs534725922	chr2:55679304-55679305	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
42	rs75132444	chr2:55679321-55679322	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
43	rs554504576	chr2:55679374-55679375	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
44	rs201690647	chr2:55679383-55679384	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
45	rs115932690	chr2:55679401-55679402	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
46	rs543519381	chr2:55679421-55679422	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs563395695	chr2:55679471-55679472	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
48	rs2061032	chr2:55679490-55679491	Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
49	rs185711636	chr2:55679503-55679504	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
50	rs189178920	chr2:55679504-55679505	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:80)

Disease	PMID	Source
Medulloblastoma	21979893	CNVD
Lynch syndrome	18415027	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Ovarian neoplasms	16753589	CNVD
Glioblastoma multiforme	17387387	CNVD
Neuroblastoma	17533364	CNVD
Neuroblastoma	18923191	CNVD
Endometrial cancer	22040021	CNVD
Adrenal tumor	17535989	CNVD
Breast cancer	21264507	CNVD
Basal cell lymphoma	17053054	CNVD
Medulloblastoma	17522785	CNVD
Cancer	23418310	CNVD
Breast cancer	17603634	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Ependymoma	16718352	CNVD
lymphocytic leukemia	21291569	CNVD
Prostate cancer	18632612	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Intellectual disability	22102821	CNVD
Cancer	20164919	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Follicular lymphoma	20505157	CNVD
Autism	17483303	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Esophageal adenocarcinoma	18519675	CNVD
Medulloblastoma	20607354	CNVD
Leukemia	18628472	CNVD
Autism	22495311	CNVD
Autism	18522746	CNVD
Breast cancer	21785460	CNVD
Lung cancer	18438408	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Neuroblastoma	21508638	CNVD
Neurodevelopmental disorder	22521361	CNVD
Melanoma	18172304	CNVD
Cancer	16751803	CNVD
Colorectal cancer	16272173	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Williams Syndrome	20824207	CNVD
Breast cancer	16272173	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Ovarian cancer	21720365	CNVD
abnormal development	18461090	CNVD
Retinoblastoma	22278416	CNVD
Cancer	21183584	CNVD
Breast cancer	16397240	CNVD
Chronic lymphocytic leukemia	17053054	CNVD
Hereditary non-polyposis colorectal cancer	19566914	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
small cell lung cancer	20016488	CNVD
Developmental delay	21147756	CNVD
Mental retardation	19951919	CNVD
Myelofibrosis	22110671	CNVD
Microcephaly	20799320	CNVD
camptodactyly	20799320	CNVD
cognitive delay	20799320	CNVD
prenatal and postnatal growth deficiency	20799320	CNVD
ptosis of eyelids	20799320	CNVD
Maculopathy	20981449	CNVD
2p16.1 microdeletion syndrome	22283845	CNVD
Autism	22579565	CNVD
Autism	16963482	CNVD
Autism	21750575	CNVD
idiopathic intellectual disability	16963482	CNVD
Carcinoma ex pleomorphic adenoma	18828159	CNVD
Multiple myeloma	16616336	CNVD
Follicular lymphoma	17699855	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Ependymoma	20639864	CNVD
Melanoma	20877625	CNVD
Breast cancer	22522925	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55678600-55679200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr2:55678800-55679200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:55678800-55679200	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr2:55678800-55679200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr2:55678800-55679200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr2:55678800-55679200	Enhancers	NHEK	skin
7	chr2:55679200-55681400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr2:55680000-55680400	Enhancers	Fetal Kidney	kidney
9	chr2:55680000-55680600	Enhancers	GM12878-XiMat	blood
10	chr2:55681400-55681600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr2:55681400-55683400	Enhancers	Fetal Heart	heart

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