Variant report

Variant	nsv968740
Chromosome Location	chr9:102937708-102938501
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-STX17-5	chr9:102937460-102938338	NONHSAT133711

Extended variants
information (count: 27 )
Associated
traits (count: 67 )

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	rs570891411	chr9:102937798-102937799	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
2	rs539569265	chr9:102937813-102937814	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
3	rs558309862	chr9:102937831-102937832	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
4	rs146046421	chr9:102937857-102937858	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
5	rs540918011	chr9:102937903-102937904	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
6	rs554801895	chr9:102937906-102937907	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
7	rs574653142	chr9:102937947-102937948	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
8	rs144131805	chr9:102937956-102937957	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
9	rs563157776	chr9:102937969-102937970	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
10	rs77073122	chr9:102937976-102937977	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
11	rs2416986	chr9:102937981-102937982	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
12	rs571169850	chr9:102937982-102937983	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
13	rs545946428	chr9:102937986-102937987	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
14	rs192695811	chr9:102938007-102938008	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
15	rs528740666	chr9:102938061-102938062	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
16	rs111232501	chr9:102938097-102938098	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
17	rs548504554	chr9:102938134-102938135	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
18	rs532288113	chr9:102938138-102938139	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
19	rs568699881	chr9:102938152-102938153	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
20	rs550129402	chr9:102938179-102938180	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
21	rs531127847	chr9:102938180-102938181	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
22	rs73656955	chr9:102938207-102938208	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
23	rs570541155	chr9:102938227-102938228	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
24	rs146006000	chr9:102938251-102938252	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
25	rs553092447	chr9:102938356-102938357	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs557250966	chr9:102938376-102938377	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs375251744	chr9:102938486-102938487	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:67)

Disease	PMID	Source
Chordoma	18071362	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Chordoma	21602918	CNVD
Renal cell carcinoma	18592004	CNVD
Developmental delay	19490664	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Pleomorphic xanthoastrocytoma	20730472	CNVD
Medulloblastoma	21979893	CNVD
microdeletion syndrome	16199537	CNVD
Ovarian cancer	21720365	CNVD
Non-syndromic sensorineural hearing loss	21030649	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Cancer	20164919	CNVD
Urothelial carcinoma	21177765	CNVD
Renal cell carcinoma	21668985	CNVD
Autism	22495311	CNVD
Melanoma	18172304	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Cancer	16751803	CNVD
Myelofibrosis	22110671	CNVD
lymphocytic leukemia	21291569	CNVD
Leukemia	17361228	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Glioblastoma	16823260	CNVD
Leukemia	18688285	CNVD
Non-small cell lung cancer	21044232	CNVD
Brain cancer	20823417	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Astrocytoma	17387387	CNVD
Glioblastoma multiforme	21080181	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Renal cell carcinoma	19461508	CNVD
Neuroblastoma	18923191	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Heart disease	21282601	CNVD
Acute promyelocytic leukemia	19109227	CNVD
Lung cancer	18438408	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Acute myeloid leukemia	21251322	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Breast cancer	17603634	CNVD
Acute myeloid leukemia	20729466	CNVD
Oral cancer	21386901	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
T-cell acute lymphoblastic leukemia	18185524	CNVD
Wilms tumour	21544195	CNVD
Prostate cancer	18632612	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Gastric cancer	17908304	CNVD
Gastrointestinal stromal cancer	20877625	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
small cell lung cancer	20016488	CNVD
Cardiac fibroma	18329553	CNVD
Breast cancer	17133270	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
T-cell acute lymphoblastic leukemia	19406988	CNVD
Fukuyama congenital muscular dystrophy	21572526	CNVD
Testicular germ cell tumor	18059402	CNVD
Acute lymphoblastic leukemia	18458336	CNVD
Mantle cell lymphoma	19029149	CNVD
Intracranial aneurysm	16715129	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:102912400-102937800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr9:102914600-102940600	Weak transcription	HSMMtube	muscle
3	chr9:102916200-102941400	Weak transcription	HepG2	liver
4	chr9:102916400-102938200	Weak transcription	Adipose Nuclei	Adipose
5	chr9:102921200-102938800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr9:102929600-102938000	Weak transcription	Thymus	Thymus
7	chr9:102930600-102940000	Weak transcription	Pancreas	Pancrea
8	chr9:102930800-102938000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr9:102931000-102941000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr9:102932200-102941200	Weak transcription	Stomach Smooth Muscle	stomach
11	chr9:102932600-102939800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr9:102933400-102939000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr9:102933400-102942000	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr9:102933600-102941000	Weak transcription	Spleen	Spleen
15	chr9:102934000-102939200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr9:102934200-102941200	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr9:102934600-102938200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
18	chr9:102935200-102938200	ZNF genes & repeats	Fetal Muscle Trunk	muscle
19	chr9:102935400-102939000	ZNF genes & repeats	Fetal Lung	lung
20	chr9:102935400-102939200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr9:102935400-102952000	Weak transcription	Small Intestine	intestine
22	chr9:102935600-102938400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr9:102935800-102939400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr9:102936200-102938400	Weak transcription	K562	blood
25	chr9:102936200-102939000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr9:102936200-102939800	Weak transcription	Psoas Muscle	Psoas
27	chr9:102936200-102941600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr9:102936400-102939400	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr9:102936400-102939400	Weak transcription	Fetal Kidney	kidney
30	chr9:102936400-102940600	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr9:102936400-102941000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr9:102936400-102952600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr9:102936600-102939000	Weak transcription	A549	lung
34	chr9:102936600-102939000	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr9:102936600-102939600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr9:102937000-102940000	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr9:102937000-102940400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr9:102937200-102938200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr9:102937200-102938200	Strong transcription	Left Ventricle	heart
40	chr9:102937200-102939000	Weak transcription	Placenta	Placenta
41	chr9:102937200-102940400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr9:102937400-102938400	Strong transcription	Liver	Liver
43	chr9:102937400-102939000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr9:102937400-102939600	Strong transcription	Ovary	ovary
45	chr9:102937400-102939800	Weak transcription	Right Ventricle	heart
46	chr9:102937400-102940600	ZNF genes & repeats	Fetal Muscle Leg	muscle
47	chr9:102937600-102937800	Strong transcription	Aorta	Aorta
48	chr9:102937600-102938600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr9:102937600-102939000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr9:102937600-102939000	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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