Variant report

Variant	nsv580022
Chromosome Location	chr19:52889544-52890809
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	chr19:52875265..52876916-chr19:52889763..52892567,2	MCF-7	breast:

Extended variants
information (count: 48 )
Associated
traits (count: 66 )

Variant overlapped rSNPs/rCNVs (count:48 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs116199606	chr19:52889604-52889605	ZNF genes & repeats Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs373373884	chr19:52889637-52889638	ZNF genes & repeats Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs368158377	chr19:52889669-52889670	ZNF genes & repeats Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs546978926	chr19:52889681-52889682	ZNF genes & repeats Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs7260085	chr19:52889687-52889688	ZNF genes & repeats Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
6	rs532007426	chr19:52889697-52889698	ZNF genes & repeats Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs12985084	chr19:52889715-52889716	ZNF genes & repeats Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs7259863	chr19:52889719-52889720	ZNF genes & repeats Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
9	rs561158349	chr19:52889782-52889783	ZNF genes & repeats Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs145242317	chr19:52889783-52889784	ZNF genes & repeats Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs11883308	chr19:52889803-52889804	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
12	rs555166497	chr19:52889809-52889810	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs186891840	chr19:52889814-52889815	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs191341952	chr19:52889865-52889866	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs370504982	chr19:52889875-52889876	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs181333263	chr19:52889881-52889882	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs149110268	chr19:52889883-52889884	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs185323483	chr19:52889919-52889920	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs74974606	chr19:52889943-52889944	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs189684599	chr19:52889949-52889950	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs183447845	chr19:52889958-52889959	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs560308215	chr19:52889970-52889971	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs528588272	chr19:52889980-52889981	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs12977007	chr19:52890010-52890011	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
25	rs368383994	chr19:52890056-52890057	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs71180452	chr19:52890075-52890076	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs34830840	chr19:52890186-52890187	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
28	rs139511606	chr19:52890280-52890281	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs571641083	chr19:52890333-52890334	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs371780367	chr19:52890406-52890407	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs187784987	chr19:52890423-52890424	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs529815160	chr19:52890429-52890430	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs377222252	chr19:52890438-52890439	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs12978111	chr19:52890454-52890455	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
35	rs569421732	chr19:52890464-52890465	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs111410636	chr19:52890482-52890483	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs554789110	chr19:52890487-52890488	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs372801518	chr19:52890521-52890522	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs530423643	chr19:52890573-52890574	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs375428120	chr19:52890625-52890626	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs548452114	chr19:52890631-52890632	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs567094401	chr19:52890632-52890633	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs369822878	chr19:52890656-52890657	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs10646059	chr19:52890706-52890707	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs533638183	chr19:52890713-52890714	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs558256646	chr19:52890770-52890771	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs570095484	chr19:52890784-52890785	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs567881441	chr19:52890806-52890807	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	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
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
Adrenocortical carcinoma	18281524	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Lung cancer	18438408	CNVD
Basal cell lymphoma	19029149	CNVD
Diffuse large b-cell lymphoma	19029149	CNVD
Colorectal cancer	16272173	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Ovarian cancer	21781307	CNVD
Neuroblastoma	20406844	CNVD
Cancer	20164920	CNVD
Melanoma	17363583	CNVD
Breast cancer	21785460	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52876200-52889600	ZNF genes & repeats	Fetal Kidney	kidney
2	chr19:52876200-52889800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr19:52876200-52889800	ZNF genes & repeats	Fetal Brain Female	brain
4	chr19:52876200-52890000	ZNF genes & repeats	Ovary	ovary
5	chr19:52876200-52890600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr19:52876200-52890600	ZNF genes & repeats	Fetal Lung	lung
7	chr19:52876200-52890800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr19:52876200-52890800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
9	chr19:52876200-52890800	ZNF genes & repeats	Liver	Liver
10	chr19:52876200-52893400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
11	chr19:52876200-52893800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr19:52876200-52894000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr19:52876200-52894000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr19:52876200-52894200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr19:52876200-52895000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
16	chr19:52876400-52890600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
17	chr19:52876400-52891000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr19:52877400-52893800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
19	chr19:52877800-52889800	ZNF genes & repeats	Fetal Muscle Leg	muscle
20	chr19:52877800-52894200	ZNF genes & repeats	Adipose Nuclei	Adipose
21	chr19:52879000-52889800	ZNF genes & repeats	Primary B cells from cord blood	blood
22	chr19:52879000-52889800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr19:52879000-52890600	ZNF genes & repeats	Colon Smooth Muscle	Colon
24	chr19:52879600-52890400	ZNF genes & repeats	Brain Germinal Matrix	brain
25	chr19:52880200-52890600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr19:52880400-52893800	ZNF genes & repeats	Fetal Muscle Trunk	muscle
27	chr19:52882000-52890600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
28	chr19:52884600-52889800	ZNF genes & repeats	Dnd41	blood
29	chr19:52885600-52889800	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
30	chr19:52885800-52889600	ZNF genes & repeats	Brain Cingulate Gyrus	brain
31	chr19:52885800-52889800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr19:52885800-52890600	ZNF genes & repeats	Osteobl	bone
33	chr19:52885800-52890800	ZNF genes & repeats	Brain Hippocampus Middle	brain
34	chr19:52886000-52893400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr19:52886400-52889800	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr19:52886600-52889800	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr19:52886600-52889800	ZNF genes & repeats	Gastric	stomach
38	chr19:52886600-52889800	ZNF genes & repeats	Left Ventricle	heart
39	chr19:52886600-52890000	ZNF genes & repeats	Aorta	Aorta
40	chr19:52886600-52890600	ZNF genes & repeats	Rectal Smooth Muscle	rectum
41	chr19:52886600-52890600	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
42	chr19:52888000-52897600	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr19:52888600-52891200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr19:52888600-52891400	Weak transcription	Thymus	Thymus
45	chr19:52888600-52892800	Weak transcription	Right Ventricle	heart
46	chr19:52888600-52898600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr19:52888800-52889800	Strong transcription	Fetal Heart	heart
48	chr19:52888800-52890200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr19:52888800-52891200	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr19:52888800-52891800	Weak transcription	NH-A	brain

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