Variant report

Variant	esv1826095
Chromosome Location	chr2:54562012-54567092
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	chr2:54560405..54562674-chr2:54570057..54572627,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000177994	chromatin interactions

Extended variants
information (count: 154 )
Associated
traits (count: 64 )

Variant overlapped rSNPs/rCNVs (count:154 , 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	rs55714450	chr2:54562012-54562013	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs199561868	chr2:54562014-54562015	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs550398337	chr2:54562052-54562053	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
4	rs75685641	chr2:54562069-54562070	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs376367434	chr2:54562086-54562087	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
6	rs371053414	chr2:54562120-54562121	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs181961211	chr2:54562170-54562171	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs547976452	chr2:54562180-54562181	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs567617777	chr2:54562181-54562182	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs1727535	chr2:54562182-54562183	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs115343841	chr2:54562184-54562185	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs202035598	chr2:54562199-54562200	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs368361160	chr2:54562201-54562202	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs548415265	chr2:54562239-54562240	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs186336520	chr2:54562261-54562262	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs568649412	chr2:54562296-54562297	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs10194310	chr2:54562298-54562299	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
18	rs139628159	chr2:54562308-54562309	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs553949190	chr2:54562309-54562310	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs13000039	chr2:54562343-54562344	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
21	rs144362806	chr2:54562355-54562356	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
22	rs562609850	chr2:54562379-54562380	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs147830055	chr2:54562399-54562400	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
24	rs545022197	chr2:54562409-54562410	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
25	rs567752375	chr2:54562414-54562415	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs534757092	chr2:54562580-54562581	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs565535736	chr2:54562594-54562595	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
28	rs141613286	chr2:54562621-54562622	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs538675111	chr2:54562661-54562662	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
30	rs528005411	chr2:54562743-54562744	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
31	rs554650095	chr2:54562768-54562769	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs558871603	chr2:54562791-54562792	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
33	rs147071243	chr2:54562792-54562793	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs189077753	chr2:54562805-54562806	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs573453747	chr2:54562852-54562853	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs145173754	chr2:54562903-54562904	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs149150609	chr2:54562924-54562925	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
38	rs538601539	chr2:54562931-54562932	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
39	rs558538378	chr2:54562932-54562933	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
40	rs556359905	chr2:54562963-54562964	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs534118381	chr2:54563011-54563012	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
42	rs62141761	chr2:54563013-54563014	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
43	rs553811897	chr2:54563022-54563023	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
44	rs534921617	chr2:54563023-54563024	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
45	rs143388429	chr2:54563042-54563043	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
46	rs542500893	chr2:54563051-54563052	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs13405819	chr2:54563075-54563076	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
48	rs116032787	chr2:54563083-54563084	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
49	rs843670	chr2:54563104-54563105	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
50	rs564903884	chr2:54563118-54563119	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	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:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54558600-54562200	Weak transcription	HSMM	muscle
2	chr2:54558600-54562200	Weak transcription	HSMMtube	muscle
3	chr2:54558600-54562600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr2:54558600-54562800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr2:54558600-54563000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr2:54558600-54563400	Weak transcription	Aorta	Aorta
7	chr2:54558600-54563400	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr2:54558800-54562200	Weak transcription	NHLF	lung
9	chr2:54558800-54562600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr2:54558800-54562800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr2:54558800-54562800	Weak transcription	Right Atrium	heart
12	chr2:54558800-54562800	Weak transcription	Osteobl	bone
13	chr2:54558800-54563000	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr2:54558800-54563200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr2:54558800-54563200	Weak transcription	Stomach Smooth Muscle	stomach
16	chr2:54558800-54563400	Weak transcription	Colon Smooth Muscle	Colon
17	chr2:54558800-54563800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr2:54558800-54563800	Weak transcription	Adipose Nuclei	Adipose
19	chr2:54558800-54563800	Weak transcription	Brain Hippocampus Middle	brain
20	chr2:54558800-54563800	Weak transcription	Lung	lung
21	chr2:54558800-54574800	Weak transcription	Left Ventricle	heart
22	chr2:54559000-54563400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr2:54559000-54563400	Weak transcription	Brain Cingulate Gyrus	brain
24	chr2:54559000-54563400	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr2:54559000-54568400	Weak transcription	Right Ventricle	heart
26	chr2:54559200-54563600	Weak transcription	Brain Anterior Caudate	brain
27	chr2:54559400-54562400	Weak transcription	NHDF-Ad	bronchial
28	chr2:54559800-54562600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr2:54562000-54564800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr2:54562000-54565400	Enhancers	Fetal Heart	heart
31	chr2:54562200-54563800	Enhancers	HSMMtube	muscle
32	chr2:54562200-54563800	Enhancers	NHLF	lung
33	chr2:54562200-54565000	Enhancers	HSMM	muscle
34	chr2:54562400-54565000	Enhancers	NHDF-Ad	bronchial
35	chr2:54562600-54563600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr2:54562600-54564600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr2:54562600-54565400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr2:54562800-54563000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr2:54562800-54563200	Enhancers	Right Atrium	heart
40	chr2:54562800-54563800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr2:54562800-54564400	Enhancers	NH-A	brain
42	chr2:54562800-54565200	Enhancers	Osteobl	bone
43	chr2:54562800-54565400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr2:54563000-54563200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr2:54563000-54563800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr2:54563000-54564800	Enhancers	Muscle Satellite Cultured Cells	--
47	chr2:54563200-54563600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr2:54563200-54564000	Enhancers	Stomach Smooth Muscle	stomach
49	chr2:54563200-54564600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr2:54563200-54568600	Weak transcription	Right Atrium	heart

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