Variant report

Variant	nsv978826
Chromosome Location	chr19:44341014-44341514
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	chr19:44330286..44333165-chr19:44339420..44341971,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-IRGC-4	chr19:44341247-44341331	NONHSAT066634

Variant related genes	Relation type
ENSG00000159871	chromatin interactions
ENSG00000167637	chromatin interactions

Extended variants
information (count: 27 )
Associated
traits (count: 69 )

Variant overlapped rSNPs/rCNVs (count:27 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs191748367	chr19:44341017-44341018	Strong transcription ZNF genes & repeats Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
2	rs527364585	chr19:44341081-44341082	Strong transcription ZNF genes & repeats Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs547215550	chr19:44341090-44341091	Strong transcription ZNF genes & repeats Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
4	rs369988269	chr19:44341092-44341093	Strong transcription ZNF genes & repeats Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
5	rs543906771	chr19:44341096-44341097	Strong transcription ZNF genes & repeats Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
6	rs78938003	chr19:44341165-44341166	Strong transcription ZNF genes & repeats Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
7	rs183628099	chr19:44341177-44341178	Strong transcription ZNF genes & repeats Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
8	rs189019805	chr19:44341184-44341185	Strong transcription ZNF genes & repeats Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
9	rs377544306	chr19:44341186-44341187	Strong transcription ZNF genes & repeats Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
10	rs202229055	chr19:44341187-44341188	Strong transcription ZNF genes & repeats Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
11	rs370983131	chr19:44341207-44341208	Strong transcription ZNF genes & repeats Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs199848094	chr19:44341247-44341248	Strong transcription ZNF genes & repeats Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
13	rs367553149	chr19:44341251-44341252	Strong transcription ZNF genes & repeats Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
14	rs562270667	chr19:44341260-44341261	Strong transcription ZNF genes & repeats Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
15	rs145411708	chr19:44341288-44341289	Strong transcription ZNF genes & repeats Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
16	rs201943823	chr19:44341305-44341306	Strong transcription ZNF genes & repeats Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
17	rs200980282	chr19:44341308-44341309	Strong transcription ZNF genes & repeats Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
18	rs372244918	chr19:44341325-44341326	Strong transcription ZNF genes & repeats Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
19	rs570030544	chr19:44341328-44341329	Strong transcription ZNF genes & repeats Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
20	rs16976817	chr19:44341340-44341341	Strong transcription ZNF genes & repeats Weak transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
21	rs191997803	chr19:44341421-44341422	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
22	rs565976924	chr19:44341424-44341425	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
23	rs116446354	chr19:44341431-44341432	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
24	rs555101898	chr19:44341481-44341482	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
25	rs573837318	chr19:44341488-44341489	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
26	rs182107827	chr19:44341496-44341497	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
27	rs373522641	chr19:44341503-44341504	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:69)

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
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
Breast cancer	16608533	CNVD
Neuroblastoma	18923191	CNVD
Breast cancer	21364760	CNVD
Chordoma	18071362	CNVD
Urothelial carcinoma	21177765	CNVD
small cell lung cancer	20016488	CNVD
Wilms tumour	21544195	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Metanephric adenoma	20802469	CNVD
Acute myeloid leukemia	16864856	CNVD
Bladder cancer	21909424	CNVD
Medulloblastoma	16783165	CNVD
Acute myeloid leukemia	20729466	CNVD
Lung cancer	18438408	CNVD
Astrocytoma	22246337	CNVD
Ovarian cancer	22174824	CNVD
Cancer	20164920	CNVD
Multiple myeloma	16616336	CNVD
Ovarian cancer	20800559	CNVD
Ovarian clear cell carcinoma	19293255	CNVD
Myelofibrosis	22110671	CNVD
Breast cancer	16272173	CNVD
Spondylocostal dysostosis	21085971	CNVD
Nicotine metabolism	21956041	CNVD
Primary central nervous system lymphoma	21088137	CNVD
Glioblastoma multiforme	17002787	CNVD
Ovarian cancer	20844748	CNVD
Breast cancer	17133270	CNVD
Hepatocellular carcinoma	16750200	CNVD
Colorectal cancer	20459617	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:144 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44332000-44344400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr19:44332400-44343400	Weak transcription	Stomach Mucosa	stomach
3	chr19:44332600-44342400	Strong transcription	Placenta	Placenta
4	chr19:44332800-44343000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr19:44332800-44343000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr19:44332800-44343400	Strong transcription	Fetal Muscle Trunk	muscle
7	chr19:44332800-44348200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr19:44332800-44357200	ZNF genes & repeats	Liver	Liver
9	chr19:44333000-44342200	Strong transcription	Skeletal Muscle Male	skeletal muscle
10	chr19:44333200-44342200	Strong transcription	Muscle Satellite Cultured Cells	--
11	chr19:44333600-44341200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr19:44333600-44357400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr19:44333800-44343800	Strong transcription	Placenta Amnion	Placenta Amnion
14	chr19:44334000-44347400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
15	chr19:44334000-44353200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr19:44335200-44346200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr19:44335200-44357200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr19:44335200-44368200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr19:44335400-44341200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr19:44335400-44346000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr19:44335400-44357200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
22	chr19:44335400-44366600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
23	chr19:44336400-44342600	Strong transcription	Primary T killer memory cells from peripheral blood	blood
24	chr19:44336400-44342600	Strong transcription	Right Ventricle	heart
25	chr19:44336600-44342000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr19:44336600-44342600	ZNF genes & repeats	Fetal Kidney	kidney
27	chr19:44336600-44357600	ZNF genes & repeats	Adipose Nuclei	Adipose
28	chr19:44336800-44342800	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
29	chr19:44336800-44353000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
30	chr19:44336800-44356800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
31	chr19:44336800-44357200	ZNF genes & repeats	Fetal Lung	lung
32	chr19:44337200-44347800	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
33	chr19:44337800-44342400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr19:44337800-44342600	Strong transcription	HSMMtube	muscle
35	chr19:44337800-44347600	ZNF genes & repeats	Fetal Muscle Leg	muscle
36	chr19:44338000-44349600	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
37	chr19:44338000-44352800	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr19:44338200-44341200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr19:44338600-44342800	ZNF genes & repeats	Lung	lung
40	chr19:44338800-44342400	Strong transcription	Thymus	Thymus
41	chr19:44339000-44341200	Strong transcription	Brain Cingulate Gyrus	brain
42	chr19:44339000-44341400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
43	chr19:44339000-44343000	ZNF genes & repeats	Fetal Intestine Small	intestine
44	chr19:44339000-44349600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
45	chr19:44339000-44352800	ZNF genes & repeats	Rectal Smooth Muscle	rectum
46	chr19:44339000-44355400	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
47	chr19:44339200-44341200	Strong transcription	Fetal Heart	heart
48	chr19:44339200-44341200	Strong transcription	Gastric	stomach
49	chr19:44339200-44341400	ZNF genes & repeats	HSMM	muscle
50	chr19:44339200-44341600	ZNF genes & repeats	Fetal Stomach	stomach

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