Variant report

Variant	esv3456943
Chromosome Location	chr2:54563548-54569446
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54555822..54558489-chr2:54561441..54564836,3	MCF-7	breast:
2	chr2:54556162..54557934-chr2:54568229..54570513,2	K562	blood:

Variant related genes	Relation type
ENSG00000177994	chromatin interactions

Extended variants
information (count: 168 )
Associated
traits (count: 64 )

Variant overlapped rSNPs/rCNVs (count:168 , 50 per page) page: 1 2 3 4

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs532503710	chr2:54563548-54563549	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
2	rs181474376	chr2:54563552-54563553	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs565707195	chr2:54563621-54563622	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
4	rs138425013	chr2:54563638-54563639	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs547627715	chr2:54563676-54563677	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
6	rs567448289	chr2:54563694-54563695	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs536409489	chr2:54563743-54563744	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs138968026	chr2:54563747-54563748	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs116821508	chr2:54563765-54563766	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs556434429	chr2:54563788-54563789	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs541081795	chr2:54563803-54563804	Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs560963149	chr2:54563818-54563819	Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs141616151	chr2:54563822-54563823	Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs538711325	chr2:54563853-54563854	Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs369653711	chr2:54563857-54563858	Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs529857265	chr2:54563892-54563893	Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs550089650	chr2:54563903-54563904	Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs76883852	chr2:54563942-54563943	Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs563933150	chr2:54563950-54563951	Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs146228109	chr2:54563952-54563953	Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs561623255	chr2:54564021-54564022	Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
22	rs575071473	chr2:54564041-54564042	Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs543593656	chr2:54564047-54564048	Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
24	rs563566688	chr2:54564074-54564075	Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
25	rs10206939	chr2:54564091-54564092	Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
26	rs372481089	chr2:54564125-54564126	Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs552849443	chr2:54564144-54564145	Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
28	rs565694657	chr2:54564235-54564236	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs139030229	chr2:54564268-54564269	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
30	rs528436448	chr2:54564298-54564299	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
31	rs548336824	chr2:54564321-54564322	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs149447219	chr2:54564345-54564346	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
33	rs536579840	chr2:54564351-54564352	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs550123928	chr2:54564364-54564365	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs569835288	chr2:54564467-54564468	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs538847737	chr2:54564489-54564490	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs186727108	chr2:54564622-54564623	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
38	rs528719511	chr2:54564669-54564670	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
39	rs548223143	chr2:54564679-54564680	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
40	rs143874960	chr2:54564682-54564683	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs148683389	chr2:54564829-54564830	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
42	rs534601707	chr2:54564845-54564846	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs554302251	chr2:54564846-54564847	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs575054042	chr2:54564847-54564848	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs542122723	chr2:54564848-54564849	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs191626991	chr2:54564916-54564917	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs562114408	chr2:54564926-54564927	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs73933627	chr2:54564934-54564935	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
49	rs576980530	chr2:54564936-54564937	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs545988110	chr2:54564962-54564963	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:64)

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
Lung adenocarcinoma	17086460	CNVD
Retinoblastoma	22278416	CNVD
Cancer	21183584	CNVD
Breast cancer	16397240	CNVD
Lung cancer	17086460	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
Myelofibrosis	22110671	CNVD
Developmental delay	21147756	CNVD
Breast cancer	22522925	CNVD
early-passage human iPS cells	21368824	CNVD

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54558800-54563800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:54558800-54563800	Weak transcription	Adipose Nuclei	Adipose
3	chr2:54558800-54563800	Weak transcription	Brain Hippocampus Middle	brain
4	chr2:54558800-54563800	Weak transcription	Lung	lung
5	chr2:54558800-54574800	Weak transcription	Left Ventricle	heart
6	chr2:54559000-54568400	Weak transcription	Right Ventricle	heart
7	chr2:54559200-54563600	Weak transcription	Brain Anterior Caudate	brain
8	chr2:54562000-54564800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr2:54562000-54565400	Enhancers	Fetal Heart	heart
10	chr2:54562200-54563800	Enhancers	HSMMtube	muscle
11	chr2:54562200-54563800	Enhancers	NHLF	lung
12	chr2:54562200-54565000	Enhancers	HSMM	muscle
13	chr2:54562400-54565000	Enhancers	NHDF-Ad	bronchial
14	chr2:54562600-54563600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr2:54562600-54564600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr2:54562600-54565400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr2:54562800-54563800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr2:54562800-54564400	Enhancers	NH-A	brain
19	chr2:54562800-54565200	Enhancers	Osteobl	bone
20	chr2:54562800-54565400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr2:54563000-54563800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr2:54563000-54564800	Enhancers	Muscle Satellite Cultured Cells	--
23	chr2:54563200-54563600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr2:54563200-54564000	Enhancers	Stomach Smooth Muscle	stomach
25	chr2:54563200-54564600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr2:54563200-54568600	Weak transcription	Right Atrium	heart
27	chr2:54563400-54564200	Enhancers	Aorta	Aorta
28	chr2:54563400-54564200	Enhancers	Colon Smooth Muscle	Colon
29	chr2:54563400-54564400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr2:54563400-54564400	Enhancers	Brain Cingulate Gyrus	brain
31	chr2:54563400-54564400	Enhancers	Brain Inferior Temporal Lobe	brain
32	chr2:54563400-54564400	Enhancers	Placenta Amnion	Placenta Amnion
33	chr2:54563600-54564000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr2:54563600-54564200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr2:54563600-54564400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr2:54563600-54564600	Enhancers	Brain Anterior Caudate	brain
37	chr2:54563800-54564000	Flanking Active TSS	HSMMtube	muscle
38	chr2:54563800-54564200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr2:54563800-54564200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr2:54563800-54564200	Enhancers	Adipose Nuclei	Adipose
41	chr2:54563800-54564200	Enhancers	Brain Substantia Nigra	brain
42	chr2:54563800-54564200	Enhancers	Fetal Brain Female	brain
43	chr2:54563800-54564200	Enhancers	Lung	lung
44	chr2:54563800-54564400	Enhancers	Brain Angular Gyrus	brain
45	chr2:54563800-54564600	Enhancers	Brain Hippocampus Middle	brain
46	chr2:54563800-54564600	Flanking Active TSS	NHLF	lung
47	chr2:54564000-54564200	Enhancers	HSMMtube	muscle
48	chr2:54564200-54564400	Flanking Active TSS	HSMMtube	muscle
49	chr2:54564200-54565200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr2:54564200-54565200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links