Variant report

Variant	esv3435205
Chromosome Location	chr3:52867536-52867892
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	chr3:52867798..52869834-chr3:52876401..52878497,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000213533	chromatin interactions
ENSG00000248592	chromatin interactions

Extended variants
information (count: 17 )
Associated
traits (count: 92 )

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs546271894	chr3:52867554-52867555	Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
2	rs374819722	chr3:52867589-52867590	Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
3	rs60332615	chr3:52867595-52867596	Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
4	rs535286634	chr3:52867601-52867602	Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
5	rs373362350	chr3:52867603-52867604	Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
6	rs376293103	chr3:52867621-52867622	Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
7	rs369527392	chr3:52867626-52867627	Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
8	rs112903597	chr3:52867632-52867633	Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
9	rs199949354	chr3:52867641-52867642	Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
10	rs192116707	chr3:52867696-52867697	Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
11	rs6787916	chr3:52867715-52867716	Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
12	rs2276820	chr3:52867718-52867719	Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
13	rs143782627	chr3:52867731-52867732	Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
14	rs147250569	chr3:52867744-52867745	Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
15	rs376107093	chr3:52867747-52867748	Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
16	rs534325868	chr3:52867777-52867778	Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
17	rs6776876	chr3:52867811-52867812	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a

Variant related diseases (count:92)

Disease	PMID	Source
Acute myeloid leukemia	20729466	CNVD
Urothelial carcinoma	18382360	CNVD
Melanoma	18172304	CNVD
Cervical cancer	21062161	CNVD
Hirschsprung''s Disease	21712996	CNVD
Glioblastoma multiforme	21080181	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Insulin resistance	16721378	CNVD
Neuroblastoma	18664255	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Multiple myeloma	17077331	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Ewing''s sarcoma	21437220	CNVD
Neuroblastoma	21484798	CNVD
Non-small cell lung cancer	21044232	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Oral cancer	19627613	CNVD
Renal cell carcinoma	19461508	CNVD
Epithelial cancer	22065749	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Acute myeloid leukemia	16864856	CNVD
Liposarcoma	21253554	CNVD
Basal cell lymphoma	21115979	CNVD
Endometrial cancer	22040021	CNVD
Pancreatic endocrine tumor	20981439	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	17387387	CNVD
Oral cancer	21386901	CNVD
Cutaneous squamous cell carcinomas	19131950	CNVD
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Retinoblastoma	21504564	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Renal cell carcinoma	21668985	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Thoracic aortic aneurysm	21092924	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Intellectual disability	22102821	CNVD
Breast cancer	17603634	CNVD
Esophageal cancer	20955586	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Breast cancer	17133270	CNVD
Uveal melanoma	20484589	CNVD
Autism	22495311	CNVD
Melanoma	20688739	CNVD
Acute myeloid leukemia	21251322	CNVD
Hepatocellular carcinoma	16750200	CNVD
Cancer	21183584	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Bipolar disorder	20877625	CNVD
Bipolar disorder	21956041	CNVD
Bipolar disorder	22241247	CNVD
Biliary cancer	18923514	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Malignant mesothelioma	18160781	CNVD
Pleural malignant mesothelioma	18160781	CNVD
Prostate cancer	18632612	CNVD
Breast cancer	16397240	CNVD
Breast cancer	22032731	CNVD
Non-small cell lung cancer	20864512	CNVD
Colorectal cancer	16912164	CNVD
Non-small cell lung cancer	19010865	CNVD
Colorectal cancer	16272173	CNVD
Non-muscle invasive bladder neoplasm	19445696	CNVD
Breast cancer	21785460	CNVD
Neuroblastoma	17327916	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Chronic lymphocytic leukemia	20421269	CNVD
Septo-optic dysplasia	21572526	CNVD
Biliary cancer	19435499	CNVD
Squamous cell cancer	20885788	CNVD
Myelofibrosis	22110671	CNVD
Urothelial cell carcinoma	18451213	CNVD
Ventriculomegaly	21325761	CNVD
Breast cancer	16608533	CNVD
Prostate cancer	21965145	CNVD
Cancer	21129771	CNVD
Congenital diaphragmatic hernia	21085971	CNVD
Lung cancer	16618734	CNVD
Neuroblastoma	19686582	CNVD
Renal cell carcinoma	18765545	CNVD
Adrenocortical carcinoma	18281524	CNVD
Pancreatic ductal adenocarcinoma	19077451	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52850200-52868400	Weak transcription	Colonic Mucosa	Colon
2	chr3:52852200-52869200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr3:52852800-52869200	Weak transcription	Primary B cells from cord blood	blood
4	chr3:52853000-52868000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr3:52854200-52874200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr3:52854800-52869200	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr3:52854800-52888400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr3:52856000-52875000	Weak transcription	Fetal Intestine Large	intestine
9	chr3:52856400-52868200	Weak transcription	Fetal Lung	lung
10	chr3:52857000-52868600	Weak transcription	Primary B cells from peripheral blood	blood
11	chr3:52858000-52867800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr3:52858000-52868400	Weak transcription	Brain Germinal Matrix	brain
13	chr3:52858400-52867600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr3:52858800-52868800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr3:52858800-52868800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr3:52858800-52869200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr3:52859400-52869000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr3:52860200-52869000	Weak transcription	Fetal Intestine Small	intestine
19	chr3:52861200-52868800	Weak transcription	Lung	lung
20	chr3:52862000-52869200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr3:52862000-52882600	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr3:52863200-52872600	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr3:52864400-52875800	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr3:52865000-52867800	Enhancers	Psoas Muscle	Psoas
25	chr3:52865000-52869400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr3:52865200-52869000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr3:52865600-52867600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr3:52865600-52874200	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr3:52865600-52875200	Weak transcription	Dnd41	blood
30	chr3:52865800-52869000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr3:52865800-52878600	Weak transcription	Small Intestine	intestine
32	chr3:52866000-52868200	Weak transcription	Brain Angular Gyrus	brain
33	chr3:52866000-52868400	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr3:52866000-52869800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr3:52866000-52884800	Weak transcription	HMEC	breast
36	chr3:52866200-52867600	Weak transcription	Right Atrium	heart
37	chr3:52866200-52867800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr3:52866200-52868200	Weak transcription	Ovary	ovary
39	chr3:52866200-52868400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr3:52866200-52868600	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
41	chr3:52866200-52869000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr3:52866200-52869200	Weak transcription	Placenta	Placenta
43	chr3:52866200-52869600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr3:52866200-52870200	Weak transcription	Gastric	stomach
45	chr3:52866200-52872600	Weak transcription	Duodenum Mucosa	Duodenum
46	chr3:52866200-52872600	Weak transcription	Esophagus	oesophagus
47	chr3:52866200-52885200	Weak transcription	NHEK	skin
48	chr3:52866400-52867600	Strong transcription	Brain Anterior Caudate	brain
49	chr3:52866400-52867800	Weak transcription	Left Ventricle	heart
50	chr3:52866400-52867800	Weak transcription	Right Ventricle	heart

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