Variant report

Variant	nsv606428
Chromosome Location	chr7:25360909-25362030
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NPVF-1	chr7:25360921-25361135	XLOC_006379

Variant related genes	Relation type
TOMM34	miRNA target sites

Extended variants
information (count: 40 )
Associated
traits (count: 77 )

Variant overlapped rSNPs/rCNVs (count:40 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs13228488	chr7:25360909-25360910	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs13438356	chr7:25360930-25360931	Weak transcription Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
3	rs553565521	chr7:25360944-25360945	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
4	rs150172075	chr7:25360963-25360964	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
5	rs542636921	chr7:25360973-25360974	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
6	rs374410210	chr7:25360980-25360981	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
7	rs562819453	chr7:25360981-25360982	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
8	rs6975929	chr7:25361017-25361018	Enhancers Weak transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
9	rs545238898	chr7:25361111-25361112	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
10	rs6958063	chr7:25361118-25361119	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
11	rs562065186	chr7:25361165-25361166	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs527660158	chr7:25361202-25361203	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs146763963	chr7:25361234-25361235	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs916844	chr7:25361257-25361258	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
15	rs140386524	chr7:25361330-25361331	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs372787750	chr7:25361367-25361368	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs569219803	chr7:25361397-25361398	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs916843	chr7:25361410-25361411	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs183914645	chr7:25361430-25361431	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs76137708	chr7:25361451-25361452	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs544298281	chr7:25361463-25361464	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs540055877	chr7:25361471-25361472	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs2893198	chr7:25361541-25361542	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
24	rs116382604	chr7:25361542-25361543	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs10235936	chr7:25361548-25361549	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
26	rs187628298	chr7:25361567-25361568	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs10235957	chr7:25361587-25361588	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
28	rs190851084	chr7:25361690-25361691	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs76226148	chr7:25361706-25361707	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs137881253	chr7:25361710-25361711	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs368862853	chr7:25361892-25361893	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs567069622	chr7:25361894-25361895	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs58377658	chr7:25361915-25361916	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs200039305	chr7:25361955-25361956	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs115038894	chr7:25361961-25361962	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs560636946	chr7:25361976-25361977	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs556232644	chr7:25362002-25362003	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs529309534	chr7:25362027-25362028	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs542629512	chr7:25362028-25362029	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs10236778	chr7:25362030-25362031	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a

Variant related diseases (count:77)

Disease	PMID	Source
Urothelial carcinoma	18382360	CNVD
Medulloblastoma	21979893	CNVD
Lynch syndrome	18415027	CNVD
Biliary cancer	19435499	CNVD
Cancer	16751803	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
Wilms tumour	21544195	CNVD
Glioblastoma multiforme	17387387	CNVD
Astrocytoma	17387387	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Neuroblastoma	18923191	CNVD
Glioma	21971842	CNVD
Glioblastoma multiforme	21080181	CNVD
Liposarcoma	21253554	CNVD
Oligodendroglial tumors	17285580	CNVD
Oral cancer	21386901	CNVD
colon cancer	17210682	CNVD
Lung adenocarcinoma	21810691	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Colorectal cancer	19359472	CNVD
Hypothalamic hamartomas	18252217	CNVD
Human rectal carcinomas	16397240	CNVD
Peripheral t-cell lymphoma	19118030	CNVD
Medulloblastoma	18056178	CNVD
Basal cell lymphoma	17170743	CNVD
Ewing''s sarcoma	21437220	CNVD
Thyroid cancer	19087340	CNVD
Seminomas	18059402	CNVD
Testicular cancer	18059402	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Autism	19415332	CNVD
Pleomorphic xanthoastrocytoma	20730472	CNVD
T-cell lymphomas	19863542	CNVD
Malaria	21533027	CNVD
Melanoma	18172304	CNVD
Renal cell carcinoma	19461508	CNVD
head and neck squamous cell carcinoma	19289630	CNVD
Stenocardia	21860640	CNVD
Vasospasm	21860640	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Ewing''s sarcoma	17952124	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Breast cancer	21364760	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Lung cancer	18438408	CNVD
small cell lung cancer	20016488	CNVD
Leukemia	23979775	CNVD
lymphocytic leukemia	21291569	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Autism	22495311	CNVD
Prostate cancer	16573809	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Gastrointestinal stromal cancer	20877625	CNVD
Cancer	21637783	CNVD
Squamous cell cancer	20885788	CNVD
Breast cancer	16397240	CNVD
Non-small cell lung cancer	21829676	CNVD
Glioblastoma multiforme	17002787	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Glioblastoma multiforme	18628472	CNVD
Non-syndromic sensorineural hearing loss	22570644	CNVD
Cancer	21183584	CNVD
abnormal development	18461090	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Breast cancer	21785460	CNVD
Lung cancer	16773561	CNVD
Schizophrenia	19546859	CNVD
Follicular lymphoma	20505157	CNVD
Williams-beuren syndrome	22470819	CNVD
Pleomorphic liposarcoma	18784837	CNVD
Colorectal cancer	16774939	CNVD
Myelofibrosis	22110671	CNVD
Colorectal cancer	21645411	CNVD
Lung adenocarcinoma	17086460	CNVD
Colorectal cancer	19455253	CNVD

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:25355400-25361000	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr7:25356400-25361000	Weak transcription	Fetal Lung	lung
3	chr7:25358200-25362200	Enhancers	Ovary	ovary
4	chr7:25358400-25361000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr7:25358800-25361200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr7:25358800-25364600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr7:25360000-25361600	Enhancers	Pancreas	Pancrea
8	chr7:25360000-25361600	Enhancers	Sigmoid Colon	Sigmoid Colon
9	chr7:25360600-25361400	Enhancers	Fetal Intestine Small	intestine
10	chr7:25360800-25361600	Enhancers	Duodenum Mucosa	Duodenum
11	chr7:25360800-25361600	Enhancers	Fetal Intestine Large	intestine
12	chr7:25361000-25361200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr7:25361000-25361200	Enhancers	Liver	Liver
14	chr7:25361000-25361400	Enhancers	Brain Substantia Nigra	brain
15	chr7:25361000-25361400	Enhancers	Fetal Heart	heart
16	chr7:25361000-25361400	Enhancers	Fetal Lung	lung
17	chr7:25361000-25361600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr7:25361000-25361600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr7:25361000-25361600	Enhancers	Rectal Mucosa Donor 29	rectum
20	chr7:25361200-25361600	Enhancers	H1 Cell Line	embryonic stem cell
21	chr7:25361200-25361600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr7:25361200-25361800	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr7:25361200-25362600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr7:25361400-25363400	Weak transcription	Fetal Intestine Small	intestine
25	chr7:25361600-25361800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
26	chr7:25361600-25369400	Weak transcription	Pancreas	Pancrea
27	chr7:25362000-25362600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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