Variant report

Variant	esv3389987
Chromosome Location	chr19:39851930-39852345
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:39851556..39853309-chr19:39879754..39881841,2	K562	blood:
2	chr19:39851453..39853087-chr19:39880088..39881805,2	MCF-7	breast:
3	chr19:39845171..39847406-chr19:39852212..39854156,2	MCF-7	breast:
4	chr19:39850438..39852750-chr19:39855800..39859218,3	MCF-7	breast:
5	chr19:39852271..39854551-chr19:39902841..39904551,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000090924	chromatin interactions
ENSG00000179134	chromatin interactions
ENSG00000006712	chromatin interactions

Extended variants
information (count: 23 )
Associated
traits (count: 66 )

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs181591141	chr19:39851942-39851943	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
2	rs538170051	chr19:39851953-39851954	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs550559195	chr19:39851979-39851980	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
4	rs386809181	chr19:39851985-39851986	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs10424274	chr19:39851986-39851987	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
6	rs62119694	chr19:39851995-39851996	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs557849404	chr19:39852030-39852031	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs533708101	chr19:39852031-39852032	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs146134490	chr19:39852032-39852033	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs377596308	chr19:39852041-39852042	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs370956184	chr19:39852065-39852066	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs113101025	chr19:39852084-39852085	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs574246133	chr19:39852117-39852118	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs544963878	chr19:39852210-39852211	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs562428936	chr19:39852219-39852220	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
16	rs577715700	chr19:39852241-39852242	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
17	rs545097775	chr19:39852281-39852282	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
18	rs57162859	chr19:39852286-39852287	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
19	rs527418790	chr19:39852289-39852290	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
20	rs548885953	chr19:39852292-39852293	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
21	rs561184940	chr19:39852318-39852319	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
22	rs531464364	chr19:39852322-39852323	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
23	rs373406154	chr19:39852345-39852346	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:66)

Disease	PMID	Source
Myelodysplastic syndrome	17634407	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Chordoma	21602918	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Cancer	21637783	CNVD
Retinoblastoma	21504564	CNVD
Medulloblastoma	21979893	CNVD
Ovarian cancer	21720365	CNVD
Cancer	20164919	CNVD
Thoracic aortic aneurysm	21092924	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Prostate cancer	18632612	CNVD
Autism	22495311	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Ductal carcinoma	22052326	CNVD
Pleomorphic liposarcoma	18784837	CNVD
Congenital nephrotic syndrome	18421352	CNVD
Astrocytoma	17934521	CNVD
Leukemia	17361228	CNVD
Adenoid cystic carcinoma	17372589	CNVD
Breast cancer	21858162	CNVD
Breast cancer	17603634	CNVD
Glioma	21971842	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Endometrial cancer	22040021	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Oligodendroglial tumors	17285580	CNVD
renal disease	20603712	CNVD
Salivary gland adenoid cystic carcinoma	17545515	CNVD
Disorders of sex development	21048976	CNVD
Ovarian cancer	22174824	CNVD
Breast cancer	16608533	CNVD
Neuroblastoma	18923191	CNVD
Breast cancer	21364760	CNVD
Invasive pancreatic ductal carcinoma	18765526	CNVD
Rhabdomyosarcoma	16790082	CNVD
Chordoma	18071362	CNVD
Urothelial carcinoma	21177765	CNVD
small cell lung cancer	20016488	CNVD
Wilms tumour	21544195	CNVD
Mental retardation	19951919	CNVD
19q13.11 deletion syndrome	22378287	CNVD
Myelofibrosis	22110671	CNVD
Breast cancer	21045282	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Ovarian neoplasms	16753589	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Metanephric adenoma	20802469	CNVD
Acute myeloid leukemia	16864856	CNVD
Lung cancer	21569311	CNVD
Bladder cancer	21909424	CNVD
Medulloblastoma	16783165	CNVD
Breast cancer	21509527	CNVD
Gastric cancer	18160780	CNVD
Hepatocellular carcinoma	16750200	CNVD
Basal cell lymphoma	19029149	CNVD
Breast cancer	20409316	CNVD
Diffuse large b-cell lymphoma	19029149	CNVD
Multiple myeloma	16616336	CNVD
Renal cell carcinoma	18765545	CNVD
Acute myeloid leukemia	20729466	CNVD
Lung cancer	18438408	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD

Chromatin state (count:141 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39834200-39859200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr19:39834800-39852800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr19:39834800-39852800	Strong transcription	Fetal Muscle Trunk	muscle
4	chr19:39834800-39880000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr19:39835600-39853600	Strong transcription	Placenta	Placenta
6	chr19:39835800-39880200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr19:39835800-39880200	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr19:39836200-39880400	Strong transcription	Primary T cells from cord blood	blood
9	chr19:39836400-39862600	Strong transcription	Duodenum Mucosa	Duodenum
10	chr19:39836600-39864000	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr19:39836600-39880400	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr19:39836600-39880400	Strong transcription	Fetal Brain Female	brain
13	chr19:39836800-39852000	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr19:39836800-39852600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr19:39837400-39880000	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr19:39837600-39863600	Strong transcription	Fetal Intestine Small	intestine
17	chr19:39837800-39854400	Strong transcription	Fetal Stomach	stomach
18	chr19:39837800-39855400	Strong transcription	Sigmoid Colon	Sigmoid Colon
19	chr19:39838000-39880000	Strong transcription	Brain Germinal Matrix	brain
20	chr19:39838200-39858200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr19:39838200-39858200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr19:39838200-39862600	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr19:39838400-39853200	Strong transcription	A549	lung
24	chr19:39838600-39852600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr19:39838600-39880400	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr19:39838800-39880200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr19:39839000-39857600	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr19:39839000-39858200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr19:39839200-39852600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr19:39839200-39853400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr19:39839200-39879200	Strong transcription	Dnd41	blood
32	chr19:39841000-39852600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr19:39841400-39852200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr19:39841600-39880000	Strong transcription	Fetal Intestine Large	intestine
35	chr19:39841800-39855400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
36	chr19:39842000-39852000	Strong transcription	H9 Cell Line	embryonic stem cell
37	chr19:39842000-39864200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr19:39842000-39880000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
39	chr19:39842200-39880200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr19:39842200-39880400	Strong transcription	Primary neutrophils fromperipheralblood	blood
41	chr19:39842400-39853200	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr19:39842400-39856600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr19:39842400-39862400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr19:39842400-39880400	Strong transcription	Thymus	Thymus
45	chr19:39842600-39854000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr19:39842600-39854600	Strong transcription	Primary T helper cells PMA-I stimulated	--
47	chr19:39842600-39855400	Strong transcription	Fetal Thymus	thymus
48	chr19:39842600-39880400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr19:39842800-39854600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr19:39842800-39855600	Strong transcription	Primary T cells fromperipheralblood	blood

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