Variant report

Variant	esv20543
Chromosome Location	chr19:55600088-55600754
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:55598098..55602192-chr19:55668353..55672028,4	K562	blood:
2	chr19:55392520..55393347-chr19:55599997..55600552,2	K562	blood:
3	chr19:55590464..55596493-chr19:55598673..55602443,7	MCF-7	breast:
4	chr19:55599844..55600585-chr19:55657438..55658005,2	K562	blood:
5	chr19:55591753..55593275-chr19:55598361..55600388,2	MCF-7	breast:
6	chr19:55599509..55600587-chr19:55671358..55672598,4	K562	blood:
7	chr19:55599701..55601283-chr19:55870959..55872935,2	K562	blood:

Variant related genes	Relation type
ENSG00000267577	chromatin interactions
ENSG00000105048	chromatin interactions
ENSG00000267110	chromatin interactions
ENSG00000129991	chromatin interactions
ENSG00000167646	chromatin interactions
ENSG00000131037	chromatin interactions

Extended variants
information (count: 22 )
Associated
traits (count: 72 )

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs570344547	chr19:55600186-55600187	Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Active TSS	Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
2	rs536080247	chr19:55600198-55600199	Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Active TSS	Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
3	rs372651077	chr19:55600217-55600218	Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Active TSS	Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
4	rs187236968	chr19:55600240-55600241	Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Active TSS	Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
5	rs188170475	chr19:55600273-55600274	Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Active TSS	Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
6	rs574459416	chr19:55600311-55600312	Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Active TSS	Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
7	rs180884920	chr19:55600325-55600326	Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Active TSS	Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
8	rs73932300	chr19:55600369-55600370	Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Active TSS	Chromatin interactive region	6 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
9	rs36076509	chr19:55600446-55600447	Weak transcription Enhancers Strong transcription Bivalent Enhancer Genic enhancers Active TSS	Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
10	rs545465945	chr19:55600478-55600479	Weak transcription Enhancers Strong transcription Bivalent Enhancer Genic enhancers Active TSS	Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
11	rs562470332	chr19:55600498-55600499	Weak transcription Enhancers Strong transcription Bivalent Enhancer Genic enhancers Active TSS	Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
12	rs185537123	chr19:55600513-55600514	Weak transcription Enhancers Strong transcription Bivalent Enhancer Genic enhancers Active TSS	Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
13	rs541637235	chr19:55600515-55600516	Weak transcription Enhancers Strong transcription Bivalent Enhancer Genic enhancers Active TSS	Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
14	rs115703531	chr19:55600566-55600567	Weak transcription Enhancers Strong transcription Bivalent Enhancer Genic enhancers Active TSS	Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
15	rs202076332	chr19:55600586-55600587	Weak transcription Enhancers Strong transcription Bivalent Enhancer Genic enhancers Active TSS	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
16	rs2603702	chr19:55600591-55600592	Weak transcription Enhancers Strong transcription Bivalent Enhancer Genic enhancers Active TSS	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
17	rs200097886	chr19:55600594-55600595	Weak transcription Enhancers Strong transcription Bivalent Enhancer Genic enhancers Active TSS	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
18	rs202036217	chr19:55600595-55600596	Weak transcription Enhancers Strong transcription Bivalent Enhancer Genic enhancers Active TSS	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
19	rs527784784	chr19:55600606-55600607	Weak transcription Enhancers Strong transcription Bivalent Enhancer Genic enhancers Active TSS	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
20	rs547914995	chr19:55600707-55600708	Weak transcription Enhancers Strong transcription Bivalent Enhancer Genic enhancers Active TSS	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
21	rs147837040	chr19:55600709-55600710	Weak transcription Enhancers Strong transcription Bivalent Enhancer Genic enhancers Active TSS	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
22	rs2603701	chr19:55600736-55600737	Weak transcription Enhancers Strong transcription Bivalent Enhancer Genic enhancers Active TSS	Chromatin interactive region	4 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance

Variant related diseases (count:72)

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
T-cell prolymphocytic leukemia	19278963	CNVD
Prostate cancer	18632612	CNVD
Ductal carcinoma	22052326	CNVD
Congenital nephrotic syndrome	18421352	CNVD
Astrocytoma	17934521	CNVD
Leukemia	17361228	CNVD
Adenoid cystic carcinoma	17372589	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
Adenoid cystic carcinoma	18698036	CNVD
Salivary gland adenoid cystic carcinoma	17545515	CNVD
Breast cancer	16608533	CNVD
Neuroblastoma	18923191	CNVD
Chordoma	18071362	CNVD
Urothelial carcinoma	21177765	CNVD
Metanephric adenoma	20802469	CNVD
Acute myeloid leukemia	16864856	CNVD
Bladder cancer	21909424	CNVD
Medulloblastoma	16783165	CNVD
Acute myeloid leukemia	20729466	CNVD
Ovarian cancer	22174824	CNVD
Multiple myeloma	16616336	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Wilms tumour	21544195	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Congenital anomalies of the kidney and urinary tract	18852474	CNVD
Glioblastoma multiforme	17002787	CNVD
Cervical cancer	21062161	CNVD
Primary central nervous system lymphoma	21088137	CNVD
Prostate cancer	16573809	CNVD
small cell lung cancer	20016488	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Lung cancer	18438408	CNVD
Colorectal cancer	16272173	CNVD
Ovarian cancer	21781307	CNVD
Neuroblastoma	20406844	CNVD
Breast cancer	21785460	CNVD
Breast cancer	20459607	CNVD
Esophageal squamous carcinoma	18405350	CNVD
Lung adenocarcinoma	17086460	CNVD
Lung cancer	17086460	CNVD
Basal cell lymphoma	19029149	CNVD
Diffuse large b-cell lymphoma	19029149	CNVD
Myelofibrosis	22110671	CNVD
T-cell acute lymphoblastic leukemia	19406988	CNVD
Alzheimer''s disease	22166940	CNVD
Heart disease	21282601	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Glioblastoma multiforme	21922591	CNVD
Non-syndromic sensorineural hearing loss	18496225	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD
Lung squamous cell carcinoma	20842114	CNVD

Chromatin state (count:148 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:55592600-55602400	Weak transcription	Hela-S3	cervix
2	chr19:55593800-55620400	Weak transcription	HMEC	breast
3	chr19:55594800-55606000	Weak transcription	HepG2	liver
4	chr19:55598000-55602000	Weak transcription	Dnd41	blood
5	chr19:55598800-55600200	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
6	chr19:55598800-55601400	Enhancers	Fetal Heart	heart
7	chr19:55599000-55603000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr19:55599200-55600400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
9	chr19:55599200-55600400	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
10	chr19:55599200-55602000	Weak transcription	Brain Angular Gyrus	brain
11	chr19:55599200-55602400	Weak transcription	NHEK	skin
12	chr19:55599200-55626600	Weak transcription	Fetal Kidney	kidney
13	chr19:55599200-55627200	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr19:55599400-55600200	Enhancers	Right Atrium	heart
15	chr19:55599400-55600200	Enhancers	Stomach Mucosa	stomach
16	chr19:55599400-55600800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr19:55599400-55600800	Weak transcription	A549	lung
18	chr19:55599400-55601000	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr19:55599400-55601200	Enhancers	H1 Cell Line	embryonic stem cell
20	chr19:55599400-55601200	Weak transcription	Brain Substantia Nigra	brain
21	chr19:55599400-55601800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr19:55599400-55602000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr19:55599400-55602000	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr19:55599400-55604800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr19:55599400-55614800	Weak transcription	GM12878-XiMat	blood
26	chr19:55599600-55600200	Enhancers	Spleen	Spleen
27	chr19:55599600-55600400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr19:55599600-55600600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
29	chr19:55599600-55600600	Enhancers	Left Ventricle	heart
30	chr19:55599600-55600800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr19:55599600-55601600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr19:55599600-55602000	Weak transcription	Gastric	stomach
33	chr19:55599800-55600200	Enhancers	K562	blood
34	chr19:55599800-55600400	Enhancers	Fetal Brain Female	brain
35	chr19:55599800-55600400	Genic enhancers	Fetal Stomach	stomach
36	chr19:55599800-55600600	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
37	chr19:55599800-55600800	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr19:55599800-55600800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr19:55599800-55601000	Weak transcription	Ovary	ovary
40	chr19:55599800-55601200	Enhancers	Stomach Smooth Muscle	stomach
41	chr19:55599800-55601400	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr19:55599800-55601800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr19:55599800-55602000	Weak transcription	Brain Anterior Caudate	brain
44	chr19:55599800-55602000	Weak transcription	Duodenum Mucosa	Duodenum
45	chr19:55599800-55602000	Weak transcription	Lung	lung
46	chr19:55599800-55602000	Weak transcription	Psoas Muscle	Psoas
47	chr19:55599800-55602000	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr19:55599800-55602000	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr19:55599800-55602200	Weak transcription	Small Intestine	intestine
50	chr19:55599800-55602400	Weak transcription	Pancreas	Pancrea

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