Variant report

Variant	nsv960864
Chromosome Location	chr19:53618960-53619713
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:9)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:53617497..53619438-chr19:53623367..53626154,3	K562	blood:
2	chr19:53618140..53620226-chr19:53631544..53634250,2	MCF-7	breast:

(count:9 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF347-2	chr19:53619037-53619177	NONHSAT067635
2	lnc-ZNF347-2	chr19:53618957-53619064	NONHSAT067632
3	lnc-ZNF347-2	chr19:53618987-53619177	NONHSAT067633
4	lnc-ZNF347-2	chr19:53619566-53619686	NONHSAT067635
5	lnc-ZNF347-2	chr19:53619566-53619686	NONHSAT067632
6	lnc-ZNF347-2	chr19:53619513-53619686	NONHSAT067636
7	lnc-ZNF347-2	chr19:53619566-53619686	NONHSAT067634
8	lnc-ZNF347-2	chr19:53619566-53619686	NONHSAT067633
9	lnc-ZNF347-2	chr19:53619010-53619064	NONHSAT067634

No data

Variant related genes	Relation type
ENSG00000170954	chromatin interactions

Extended variants
information (count: 26 )
Associated
traits (count: 68 )

Variant overlapped rSNPs/rCNVs (count:26 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs542552434	chr19:53619009-53619010	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
2	rs561199005	chr19:53619087-53619088	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
3	rs143933836	chr19:53619117-53619118	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
4	rs185825631	chr19:53619246-53619247	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs564903783	chr19:53619288-53619289	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
6	rs547556501	chr19:53619305-53619306	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs532230181	chr19:53619308-53619309	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs3833217	chr19:53619344-53619345	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs3745180	chr19:53619391-53619392	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
10	rs146982025	chr19:53619394-53619395	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs376434770	chr19:53619415-53619416	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs79306341	chr19:53619462-53619463	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs3745181	chr19:53619465-53619466	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
14	rs535027847	chr19:53619511-53619512	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs372701338	chr19:53619546-53619547	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
16	rs546949011	chr19:53619576-53619577	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
17	rs571339410	chr19:53619599-53619600	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
18	rs538735483	chr19:53619601-53619602	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
19	rs376597389	chr19:53619605-53619606	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
20	rs138658370	chr19:53619635-53619636	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
21	rs557076828	chr19:53619636-53619637	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
22	rs141273921	chr19:53619663-53619664	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
23	rs201532894	chr19:53619666-53619667	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
24	rs575346662	chr19:53619671-53619672	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
25	rs536415065	chr19:53619689-53619690	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs138117596	chr19:53619692-53619693	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:68)

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
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	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

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53607400-53630600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr19:53607600-53620600	Weak transcription	Stomach Mucosa	stomach
3	chr19:53607600-53635000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr19:53610200-53620600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr19:53610800-53619200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
6	chr19:53611200-53621200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr19:53612600-53634200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr19:53613000-53620400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr19:53613000-53620800	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr19:53613000-53629600	Weak transcription	Fetal Heart	heart
11	chr19:53613000-53634600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr19:53613000-53635400	Weak transcription	HSMMtube	muscle
13	chr19:53614400-53619800	Strong transcription	Fetal Stomach	stomach
14	chr19:53614400-53621000	ZNF genes & repeats	Fetal Intestine Small	intestine
15	chr19:53614800-53619000	Strong transcription	Fetal Muscle Leg	muscle
16	chr19:53614800-53619200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr19:53615200-53620200	Strong transcription	Fetal Muscle Trunk	muscle
18	chr19:53615200-53620200	Strong transcription	Dnd41	blood
19	chr19:53615400-53619000	Strong transcription	Pancreatic Islets	Pancreatic Islet
20	chr19:53615400-53619200	Strong transcription	Brain Germinal Matrix	brain
21	chr19:53615400-53619400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr19:53615400-53619600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr19:53615400-53619600	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr19:53615400-53619600	Strong transcription	Placenta	Placenta
25	chr19:53615400-53619600	Strong transcription	Rectal Smooth Muscle	rectum
26	chr19:53615400-53619600	Strong transcription	Right Ventricle	heart
27	chr19:53615400-53620000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr19:53615400-53620000	Strong transcription	Cortex derived primary cultured neurospheres	brain
29	chr19:53615400-53620000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr19:53615400-53620000	Strong transcription	Brain Hippocampus Middle	brain
31	chr19:53615400-53620000	Strong transcription	Skeletal Muscle Female	skeletal muscle
32	chr19:53615400-53620000	Strong transcription	Stomach Smooth Muscle	stomach
33	chr19:53615400-53620600	Strong transcription	Fetal Brain Female	brain
34	chr19:53615400-53620600	Strong transcription	Left Ventricle	heart
35	chr19:53615400-53621000	Strong transcription	Fetal Lung	lung
36	chr19:53615400-53621400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr19:53615600-53619000	Strong transcription	Adipose Nuclei	Adipose
38	chr19:53615600-53619400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr19:53615600-53619600	Strong transcription	Colon Smooth Muscle	Colon
40	chr19:53615600-53619800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr19:53615600-53619800	Strong transcription	Fetal Thymus	thymus
42	chr19:53615600-53620400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr19:53615800-53622800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr19:53616000-53619000	Weak transcription	Primary B cells from peripheral blood	blood
45	chr19:53616000-53619000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr19:53616000-53619600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr19:53616000-53619800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr19:53616000-53619800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr19:53616000-53620000	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr19:53616000-53620400	Strong transcription	Osteobl	bone

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