Variant report

Variant	nsv960868
Chromosome Location	chr19:53707121-53708115
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	chr19:53700585..53702772-chr19:53706802..53709941,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-VN1R2-6	chr19:53707269-53707395	ENSG00000269051.1

Extended variants
information (count: 41 )
Associated
traits (count: 74 )

Variant overlapped rSNPs/rCNVs (count:41 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs565063130	chr19:53707174-53707175	ZNF genes & repeats Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs192557121	chr19:53707218-53707219	ZNF genes & repeats Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs79693304	chr19:53707237-53707238	ZNF genes & repeats Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs7249771	chr19:53707289-53707290	ZNF genes & repeats Weak transcription Strong transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
5	rs183629114	chr19:53707299-53707300	ZNF genes & repeats Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
6	rs188035454	chr19:53707358-53707359	ZNF genes & repeats Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
7	rs117004668	chr19:53707359-53707360	ZNF genes & repeats Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
8	rs533790702	chr19:53707437-53707438	ZNF genes & repeats Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs78175684	chr19:53707446-53707447	ZNF genes & repeats Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs144164595	chr19:53707465-53707466	ZNF genes & repeats Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs111524638	chr19:53707473-53707474	ZNF genes & repeats Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs537894261	chr19:53707487-53707488	ZNF genes & repeats Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs556290132	chr19:53707518-53707519	ZNF genes & repeats Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs181926131	chr19:53707534-53707535	ZNF genes & repeats Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs542838800	chr19:53707556-53707557	ZNF genes & repeats Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs28477265	chr19:53707592-53707593	ZNF genes & repeats Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
17	rs573432808	chr19:53707613-53707614	ZNF genes & repeats Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs540250933	chr19:53707660-53707661	ZNF genes & repeats Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs146523718	chr19:53707662-53707663	ZNF genes & repeats Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs140765835	chr19:53707673-53707674	ZNF genes & repeats Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs28713518	chr19:53707674-53707675	ZNF genes & repeats Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
22	rs148207513	chr19:53707699-53707700	ZNF genes & repeats Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs529926302	chr19:53707706-53707707	ZNF genes & repeats Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs548051247	chr19:53707707-53707708	ZNF genes & repeats Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs566774117	chr19:53707709-53707710	ZNF genes & repeats Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs11667222	chr19:53707739-53707740	ZNF genes & repeats Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs377255935	chr19:53707743-53707744	ZNF genes & repeats Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs552205475	chr19:53707745-53707746	ZNF genes & repeats Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs184651576	chr19:53707781-53707782	ZNF genes & repeats Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs537832845	chr19:53707796-53707797	ZNF genes & repeats Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs552515599	chr19:53707798-53707799	ZNF genes & repeats Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs577688280	chr19:53707809-53707810	ZNF genes & repeats Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs568042481	chr19:53707837-53707838	ZNF genes & repeats Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs35653121	chr19:53707838-53707839	ZNF genes & repeats Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
35	rs374775268	chr19:53707937-53707938	ZNF genes & repeats Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs11327258	chr19:53707938-53707939	ZNF genes & repeats Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs57251936	chr19:53707953-53707954	ZNF genes & repeats Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs368829813	chr19:53707954-53707955	ZNF genes & repeats Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs372551333	chr19:53707976-53707977	ZNF genes & repeats Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs17272903	chr19:53708045-53708046	ZNF genes & repeats Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
41	rs150453362	chr19:53708082-53708083	ZNF genes & repeats Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:74)

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
Myelofibrosis	22110671	CNVD
Gastric adenocarcinoma	19115996	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
Melanoma	17363583	CNVD
Breast cancer	21785460	CNVD
Adrenocortical carcinoma	18281524	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
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Lung cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53700800-53708200	Weak transcription	Fetal Heart	heart
2	chr19:53700800-53709200	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
3	chr19:53701000-53708800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr19:53701000-53709000	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
5	chr19:53701000-53709200	ZNF genes & repeats	Fetal Intestine Small	intestine
6	chr19:53701000-53709600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr19:53701000-53710000	ZNF genes & repeats	Duodenum Mucosa	Duodenum
8	chr19:53701200-53709600	ZNF genes & repeats	Primary B cells from cord blood	blood
9	chr19:53701200-53713200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr19:53701400-53708200	Weak transcription	Fetal Brain Female	brain
11	chr19:53701400-53709600	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
12	chr19:53701400-53710200	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
13	chr19:53701400-53715200	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
14	chr19:53701600-53709200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr19:53701600-53710200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr19:53701600-53715400	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
17	chr19:53701600-53720200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
18	chr19:53701600-53724800	ZNF genes & repeats	Liver	Liver
19	chr19:53701600-53725000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
20	chr19:53701600-53725000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
21	chr19:53701800-53709000	ZNF genes & repeats	Primary T cells from cord blood	blood
22	chr19:53701800-53718400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr19:53701800-53725400	ZNF genes & repeats	Adipose Nuclei	Adipose
24	chr19:53702200-53709000	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr19:53702200-53709000	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
26	chr19:53702200-53709200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr19:53702200-53710200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
28	chr19:53702200-53715200	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
29	chr19:53702400-53709600	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
30	chr19:53702400-53724800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr19:53702600-53709200	ZNF genes & repeats	Placenta	Placenta
32	chr19:53703200-53709200	ZNF genes & repeats	Fetal Intestine Large	intestine
33	chr19:53703200-53709600	ZNF genes & repeats	Lung	lung
34	chr19:53703400-53709600	ZNF genes & repeats	Primary T helper 17 cells PMA-I stimulated	--
35	chr19:53703400-53709600	ZNF genes & repeats	Esophagus	oesophagus
36	chr19:53703400-53709600	ZNF genes & repeats	Fetal Stomach	stomach
37	chr19:53703400-53715200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
38	chr19:53703600-53709600	Strong transcription	Placenta Amnion	Placenta Amnion
39	chr19:53703600-53715000	ZNF genes & repeats	Ovary	ovary
40	chr19:53704600-53707200	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr19:53704600-53708000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr19:53705200-53715000	ZNF genes & repeats	Primary B cells from peripheral blood	blood
43	chr19:53706000-53708600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr19:53706000-53709000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr19:53706000-53709800	ZNF genes & repeats	Fetal Lung	lung
46	chr19:53706200-53707400	Strong transcription	Dnd41	blood
47	chr19:53706200-53708800	ZNF genes & repeats	NHDF-Ad	bronchial
48	chr19:53706200-53709200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr19:53706200-53709200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
50	chr19:53706200-53709600	ZNF genes & repeats	Aorta	Aorta

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