Variant report

Variant	esv3523189
Chromosome Location	chr1:172686101-172686514
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	chr1:172502079..172503900-chr1:172686438..172689153,3	MCF-7	breast:
2	chr1:172575736..172579106-chr1:172685787..172690333,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000094975	chromatin interactions

Extended variants
information (count: 29 )
Associated
traits (count: 92 )

Variant overlapped rSNPs/rCNVs (count:29 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs564145213	chr1:172686102-172686103	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
2	rs528265747	chr1:172686183-172686184	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs540190504	chr1:172686191-172686192	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
4	rs561952487	chr1:172686192-172686193	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs528943099	chr1:172686198-172686199	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
6	rs550598655	chr1:172686230-172686231	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs544383355	chr1:172686231-172686232	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs539155164	chr1:172686235-172686236	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs532902256	chr1:172686236-172686237	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs561159874	chr1:172686257-172686258	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs551429732	chr1:172686324-172686325	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs551530468	chr1:172686330-172686331	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs58336468	chr1:172686335-172686336	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs375342222	chr1:172686357-172686358	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs375624327	chr1:172686373-172686374	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs566656491	chr1:172686382-172686383	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs553108731	chr1:172686390-172686391	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs568316371	chr1:172686397-172686398	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs533993030	chr1:172686419-172686420	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs557021893	chr1:172686420-172686421	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs575723737	chr1:172686421-172686422	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
22	rs545851819	chr1:172686422-172686423	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs558149522	chr1:172686430-172686431	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
24	rs2172399	chr1:172686431-172686432	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
25	rs540537768	chr1:172686434-172686435	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs376208165	chr1:172686440-172686441	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs529091186	chr1:172686452-172686453	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
28	rs376371704	chr1:172686475-172686476	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs115851098	chr1:172686482-172686483	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:92)

Disease	PMID	Source
Breast cancer	17603634	CNVD
Esophageal squamous carcinoma	21637470	CNVD
HIV/AIDS	22032296	CNVD
Schizophrenia	19415332	CNVD
Autism	22495311	CNVD
Hepatocellular carcinoma	16750200	CNVD
Liposarcoma	21253554	CNVD
Burkitt''s lymphoma	18698080	CNVD
Melanoma	18172304	CNVD
Cancer	21183584	CNVD
Multiple myeloma	16461302	CNVD
Rett syndrome	21593744	CNVD
Intellectual disability	22102821	CNVD
Cancer	20164919	CNVD
Medulloblastoma	21979893	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
Wilms tumour	21544195	CNVD
Breast cancer	17133270	CNVD
Non-small cell lung cancer	21829676	CNVD
Carcinoma ex pleomorphic adenoma	18828159	CNVD
Non-small cell lung cancer	21044232	CNVD
Cervical cancer	21063398	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	20632083	CNVD
Endometrial cancer	22040021	CNVD
Ewing''s sarcoma	21437220	CNVD
Gastrointestinal stromal cancer	20470368	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	21080181	CNVD
Hepatocellular carcinoma	22174799	CNVD
Medulloblastoma	21292688	CNVD
Phyllodes tumor	17334353	CNVD
Breast cancer	21264507	CNVD
Multiple myeloma	21628407	CNVD
Cancer	16751803	CNVD
Prostate cancer	16705090	CNVD
Neuroblastoma	19435921	CNVD
Breast cancer	17850661	CNVD
Breast cancer	16461572	CNVD
Intracranial tumor	16823260	CNVD
Medulloblastoma	18056178	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Colorectal cancer	16272173	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Neuroblastoma	21899760	CNVD
Bladder cancer	19088036	CNVD
Ovarian neoplasms	16753589	CNVD
Glioblastoma multiforme	17002787	CNVD
Breast cancer	21858162	CNVD
Retinoblastoma	19183342	CNVD
Non-small cell lung cancer	21385341	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
Breast cancer	16608533	CNVD
Ewing''s sarcoma	22429812	CNVD
Acute promyelocytic leukemia	19109227	CNVD
Chordoma	18071362	CNVD
Hepatocellular carcinoma	18803288	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	17001317	CNVD
Urothelial carcinoma	21177765	CNVD
Burkitt''s lymphoma	19759907	CNVD
Acute myeloid leukemia	21251322	CNVD
Multiple myeloma	17550852	CNVD
Prostate cancer	18632612	CNVD
Acute myeloid leukemia	20729466	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Testicular germ cell tumor	18059402	CNVD
Trisomy 5 syndrome	21098271	CNVD
Ependymoma	18628472	CNVD
Leukemia	18628472	CNVD
Breast cancer	21611746	CNVD
Neuroblastoma	18923191	CNVD
Soft tissue tumor	16732325	CNVD
Cancer	17060936	CNVD
Lung cancer	16740712	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Ewing''s sarcoma	17952124	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
Acute lymphoblastic leukemia	19100363	CNVD
Williams-beuren syndrome	16971481	CNVD
Developmental delay	21147756	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Breast cancer	20409316	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Myelofibrosis	22110671	CNVD
Breast cancer	21509527	CNVD
Breast cancer	22522925	CNVD
Pancreatic ductal adenocarcinoma	19077451	CNVD

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172683400-172689200	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr1:172684000-172688000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr1:172684000-172688400	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr1:172684000-172689000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr1:172684000-172692400	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr1:172684600-172686200	Enhancers	NHEK	skin
7	chr1:172685000-172686200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:172685000-172686800	Enhancers	Fetal Heart	heart
9	chr1:172685000-172690400	Enhancers	Placenta	Placenta
10	chr1:172685400-172686200	Enhancers	Fetal Thymus	thymus
11	chr1:172685400-172686800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr1:172685400-172687200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr1:172685400-172687400	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr1:172685400-172687400	Enhancers	HepG2	liver
15	chr1:172685400-172687600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
16	chr1:172685400-172689200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
17	chr1:172685600-172686200	Enhancers	Primary T cells fromperipheralblood	blood
18	chr1:172685600-172686200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr1:172685600-172686200	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr1:172685600-172686200	Enhancers	Thymus	Thymus
21	chr1:172685600-172686200	Enhancers	Dnd41	blood
22	chr1:172685600-172687000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr1:172685600-172687000	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr1:172685800-172686200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr1:172685800-172686200	Enhancers	Osteobl	bone
26	chr1:172685800-172686800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr1:172685800-172689000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr1:172685800-172689000	Weak transcription	Left Ventricle	heart
29	chr1:172686000-172686400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr1:172686000-172686600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr1:172686000-172687000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr1:172686000-172687000	Weak transcription	HMEC	breast
33	chr1:172686000-172687800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr1:172686000-172688400	Enhancers	Fetal Intestine Large	intestine
35	chr1:172686000-172688600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr1:172686000-172688600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr1:172686000-172688600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr1:172686000-172693600	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr1:172686200-172686600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr1:172686200-172686600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr1:172686200-172686600	Weak transcription	NHEK	skin
42	chr1:172686200-172686600	Weak transcription	Osteobl	bone
43	chr1:172686200-172687000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr1:172686200-172688400	Weak transcription	Dnd41	blood
45	chr1:172686200-172693800	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr1:172686200-172693800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr1:172686200-172693800	Weak transcription	Fetal Thymus	thymus
48	chr1:172686400-172688400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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