Variant report

Variant	esv3349261
Chromosome Location	chr3:42552619-42552986
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	chr3:42542685..42546162-chr3:42551658..42554598,5	MCF-7	breast:
2	chr3:42552045..42554738-chr3:42559579..42561082,2	K562	blood:

Variant related genes	Relation type
ENSG00000114812	chromatin interactions

Extended variants
information (count: 18 )
Associated
traits (count: 88 )

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs138863009	chr3:42552635-42552636	Weak transcription Enhancers Genic enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
2	rs553176892	chr3:42552636-42552637	Weak transcription Enhancers Genic enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs536561957	chr3:42552665-42552666	Weak transcription Enhancers Genic enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
4	rs539147789	chr3:42552668-42552669	Weak transcription Enhancers Genic enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs149416612	chr3:42552672-42552673	Weak transcription Enhancers Genic enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
6	rs554705631	chr3:42552689-42552690	Weak transcription Enhancers Genic enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs559243930	chr3:42552725-42552726	Weak transcription Enhancers Genic enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs575809948	chr3:42552735-42552736	Weak transcription Enhancers Genic enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs186156850	chr3:42552753-42552754	Weak transcription Enhancers Genic enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs561441437	chr3:42552842-42552843	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs574603965	chr3:42552869-42552870	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs540361530	chr3:42552877-42552878	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs144775033	chr3:42552887-42552888	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs148176424	chr3:42552932-42552933	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs551874699	chr3:42552937-42552938	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs373972156	chr3:42552943-42552944	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs95923	chr3:42552961-42552962	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
18	rs575669959	chr3:42552977-42552978	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:88)

Disease	PMID	Source
Glioblastoma multiforme	21080181	CNVD
Neuroblastoma	18923191	CNVD
Colorectal cancer	21297112	CNVD
Lynch syndrome	18415027	CNVD
Renal cell carcinoma	18592004	CNVD
Acute myeloid leukemia	20729466	CNVD
Urothelial carcinoma	18382360	CNVD
Melanoma	18172304	CNVD
Cervical cancer	21062161	CNVD
Hirschsprung''s Disease	21712996	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
Lung cancer	20668451	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	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
Wilms tumour	17204608	CNVD
Biliary cancer	19435499	CNVD
Non-small cell lung cancer	20864512	CNVD
Non-small cell lung cancer	21829676	CNVD
Kartagener syndrome	16639409	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Bipolar disorder	20877625	CNVD
Bipolar disorder	21956041	CNVD
Bipolar disorder	22241247	CNVD
Biliary cancer	18923514	CNVD
Breast cancer	21509527	CNVD
Melanoma	21693616	CNVD
Myelofibrosis	22110671	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
Breast cancer	20409316	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Malignant mesothelioma	18160781	CNVD
Pleural malignant mesothelioma	18160781	CNVD
Breast cancer	21364760	CNVD
abnormal development	18461090	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42545400-42553800	Enhancers	Primary T helper cells PMA-I stimulated	--
2	chr3:42546600-42553800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
3	chr3:42547200-42561800	Genic enhancers	Fetal Intestine Small	intestine
4	chr3:42547600-42579000	Weak transcription	Rectal Smooth Muscle	rectum
5	chr3:42548600-42553000	Enhancers	Stomach Mucosa	stomach
6	chr3:42548800-42553200	Enhancers	Sigmoid Colon	Sigmoid Colon
7	chr3:42549200-42561800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:42549400-42555800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr3:42549800-42553000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr3:42549800-42553200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr3:42549800-42553200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr3:42549800-42557000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr3:42549800-42560600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr3:42550000-42556000	Weak transcription	Brain Anterior Caudate	brain
15	chr3:42550000-42560400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr3:42550200-42553600	Genic enhancers	Primary T cells from cord blood	blood
17	chr3:42550200-42558200	Enhancers	Right Ventricle	heart
18	chr3:42550400-42555000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr3:42550400-42555600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr3:42550600-42555000	Enhancers	Adipose Nuclei	Adipose
21	chr3:42550600-42558800	Enhancers	Right Atrium	heart
22	chr3:42550800-42552800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr3:42550800-42553000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr3:42550800-42555600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr3:42551000-42553600	Enhancers	Fetal Intestine Large	intestine
26	chr3:42551200-42553200	Weak transcription	Spleen	Spleen
27	chr3:42551200-42559200	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr3:42551400-42554000	Enhancers	Placenta	Placenta
29	chr3:42551400-42554000	Enhancers	Monocytes-CD14+_RO01746	blood
30	chr3:42551400-42554200	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr3:42551400-42558800	Enhancers	Left Ventricle	heart
32	chr3:42551600-42553000	Enhancers	Esophagus	oesophagus
33	chr3:42551600-42553800	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr3:42551600-42555400	Enhancers	Aorta	Aorta
35	chr3:42551800-42553200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr3:42551800-42553200	Enhancers	Rectal Mucosa Donor 29	rectum
37	chr3:42551800-42553800	Enhancers	Primary T helper cells fromperipheralblood	blood
38	chr3:42551800-42554000	Enhancers	Primary T cells fromperipheralblood	blood
39	chr3:42551800-42554400	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr3:42552000-42553200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr3:42552000-42553200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr3:42552000-42553600	Enhancers	Lung	lung
43	chr3:42552200-42555600	Weak transcription	Fetal Heart	heart
44	chr3:42552200-42556400	Weak transcription	Gastric	stomach
45	chr3:42552200-42581000	Weak transcription	Pancreas	Pancrea
46	chr3:42552400-42552800	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr3:42552400-42553200	Enhancers	Small Intestine	intestine
48	chr3:42552400-42553600	Weak transcription	Colonic Mucosa	Colon
49	chr3:42552400-42554800	Enhancers	Duodenum Mucosa	Duodenum
50	chr3:42552400-42558400	Genic enhancers	Rectal Mucosa Donor 31	rectum

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