Variant report

Variant	esv3349882
Chromosome Location	chr2:56142778-56143224
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	chr2:56122074..56124706-chr2:56141826..56144202,2	MCF-7	breast:
2	chr2:56143080..56147077-chr2:56148041..56151714,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115380	chromatin interactions

Extended variants
information (count: 13 )
Associated
traits (count: 78 )

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs570066730	chr2:56142891-56142892	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs530956216	chr2:56142988-56142989	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs2868435	chr2:56142998-56142999	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Enhancers Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
4	rs2903836	chr2:56143036-56143037	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
5	rs182965327	chr2:56143069-56143070	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs539637439	chr2:56143087-56143088	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs376973916	chr2:56143107-56143108	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs145433484	chr2:56143123-56143124	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs146589015	chr2:56143153-56143154	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs535232839	chr2:56143172-56143173	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs72811716	chr2:56143174-56143175	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
12	rs575105636	chr2:56143182-56143183	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs187308263	chr2:56143223-56143224	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:78)

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
Pancreatic ductal adenocarcinoma	19077451	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:56116400-56144400	Weak transcription	Lung	lung
2	chr2:56129000-56144200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr2:56129000-56144400	Weak transcription	HSMMtube	muscle
4	chr2:56129200-56150200	Weak transcription	Pancreas	Pancrea
5	chr2:56129400-56143000	Weak transcription	NHLF	lung
6	chr2:56132000-56149000	Weak transcription	Colon Smooth Muscle	Colon
7	chr2:56135200-56143600	Weak transcription	Adipose Nuclei	Adipose
8	chr2:56135200-56146600	Weak transcription	Brain Anterior Caudate	brain
9	chr2:56135600-56143000	Weak transcription	NHEK	skin
10	chr2:56136600-56145800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr2:56137400-56149400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:56138400-56144200	Weak transcription	NH-A	brain
13	chr2:56138800-56146400	Weak transcription	A549	lung
14	chr2:56138800-56149600	Transcr. at gene 5' and 3'	HUVEC	blood vessel
15	chr2:56139000-56143600	Weak transcription	HMEC	breast
16	chr2:56140400-56142800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr2:56140400-56143600	Weak transcription	Ovary	ovary
18	chr2:56140400-56143600	Weak transcription	Right Atrium	heart
19	chr2:56140800-56143600	Weak transcription	HSMM	muscle
20	chr2:56141600-56143800	Weak transcription	Aorta	Aorta
21	chr2:56141800-56146200	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr2:56142000-56143000	Genic enhancers	Osteobl	bone
23	chr2:56142000-56143200	Enhancers	NHDF-Ad	bronchial
24	chr2:56142000-56143600	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr2:56142000-56143800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr2:56142000-56143800	Weak transcription	Fetal Stomach	stomach
27	chr2:56142200-56142800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr2:56142200-56143000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr2:56142200-56149800	Weak transcription	Gastric	stomach
30	chr2:56142400-56142800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr2:56142400-56143200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr2:56142400-56143200	Enhancers	Muscle Satellite Cultured Cells	--
33	chr2:56142400-56143600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr2:56142400-56149400	Weak transcription	Right Ventricle	heart
35	chr2:56142600-56149200	Weak transcription	Stomach Smooth Muscle	stomach
36	chr2:56142800-56143200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr2:56142800-56143600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr2:56142800-56146000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr2:56143000-56143600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr2:56143000-56144000	Transcr. at gene 5' and 3'	Osteobl	bone
41	chr2:56143000-56144600	Enhancers	NHLF	lung
42	chr2:56143000-56145800	Strong transcription	NHEK	skin
43	chr2:56143200-56144200	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr2:56143200-56144400	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr2:56143200-56144600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr2:56143200-56144600	Weak transcription	NHDF-Ad	bronchial

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