Variant report

Variant	esv3399610
Chromosome Location	chr1:171569794-171575719
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PRRC2C-5	chr1:171570022-171570952	NONHSAT007542

Extended variants
information (count: 218 )
Associated
traits (count: 92 )

Variant overlapped rSNPs/rCNVs (count:218 , 50 per page) page: 1 2 3 4 5

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs547744096	chr1:171569846-171569847	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs565822814	chr1:171569863-171569864	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs529942976	chr1:171569896-171569897	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs548030886	chr1:171569924-171569925	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs35569413	chr1:171569928-171569929	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs78772494	chr1:171569955-171569956	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs567756232	chr1:171570021-171570022	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs372666521	chr1:171570061-171570062	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
9	rs186964960	chr1:171570082-171570083	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
10	rs191006042	chr1:171570084-171570085	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
11	rs556158741	chr1:171570088-171570089	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
12	rs571335020	chr1:171570124-171570125	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
13	rs235886	chr1:171570141-171570142	Weak transcription Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
14	rs11587602	chr1:171570158-171570159	Weak transcription Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
15	rs572647350	chr1:171570178-171570179	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
16	rs60401976	chr1:171570205-171570206	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
17	rs576175369	chr1:171570206-171570207	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
18	rs113427396	chr1:171570221-171570222	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
19	rs235887	chr1:171570274-171570275	Weak transcription Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
20	rs576104865	chr1:171570275-171570276	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
21	rs113674782	chr1:171570355-171570356	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
22	rs559065758	chr1:171570361-171570362	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
23	rs543517843	chr1:171570413-171570414	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
24	rs566257023	chr1:171570503-171570504	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
25	rs374933639	chr1:171570507-171570508	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
26	rs34828746	chr1:171570508-171570509	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
27	rs564954418	chr1:171570520-171570521	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
28	rs369112369	chr1:171570521-171570522	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
29	rs541020930	chr1:171570569-171570570	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
30	rs563979135	chr1:171570585-171570586	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
31	rs559599588	chr1:171570608-171570609	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
32	rs116406213	chr1:171570609-171570610	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
33	rs111306486	chr1:171570624-171570625	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
34	rs548379423	chr1:171570632-171570633	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
35	rs74811978	chr1:171570637-171570638	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
36	rs79426027	chr1:171570638-171570639	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
37	rs183327281	chr1:171570659-171570660	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
38	rs569721669	chr1:171570724-171570725	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
39	rs372884605	chr1:171570737-171570738	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
40	rs554769782	chr1:171570872-171570873	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
41	rs115762507	chr1:171570873-171570874	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
42	rs145985142	chr1:171570878-171570879	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
43	rs532962647	chr1:171570912-171570913	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
44	rs551588111	chr1:171570944-171570945	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
45	rs60834491	chr1:171570945-171570946	Weak transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
46	rs538694526	chr1:171571064-171571065	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs553834602	chr1:171571066-171571067	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs7536695	chr1:171571078-171571079	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
49	rs536511770	chr1:171571087-171571088	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs186138401	chr1:171571094-171571095	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:92)

Disease	PMID	Source
Breast cancer	17603634	CNVD
Esophageal squamous carcinoma	21637470	CNVD
HIV/AIDS	22032296	CNVD
Schizophrenia	19415332	CNVD
Autism	22495311	CNVD
Hepatocellular carcinoma	16750200	CNVD
Liposarcoma	21253554	CNVD
Burkitt''s lymphoma	18698080	CNVD
Melanoma	18172304	CNVD
Cancer	21183584	CNVD
Multiple myeloma	16461302	CNVD
Rett syndrome	21593744	CNVD
Intellectual disability	22102821	CNVD
Cancer	20164919	CNVD
Medulloblastoma	21979893	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
Wilms tumour	21544195	CNVD
Breast cancer	17133270	CNVD
Non-small cell lung cancer	21829676	CNVD
Carcinoma ex pleomorphic adenoma	18828159	CNVD
Non-small cell lung cancer	21044232	CNVD
Cervical cancer	21063398	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	20632083	CNVD
Endometrial cancer	22040021	CNVD
Ewing''s sarcoma	21437220	CNVD
Gastrointestinal stromal cancer	20470368	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	21080181	CNVD
Hepatocellular carcinoma	22174799	CNVD
Medulloblastoma	21292688	CNVD
Phyllodes tumor	17334353	CNVD
Breast cancer	21264507	CNVD
Multiple myeloma	21628407	CNVD
Cancer	16751803	CNVD
Prostate cancer	16705090	CNVD
Neuroblastoma	19435921	CNVD
Breast cancer	17850661	CNVD
Breast cancer	16461572	CNVD
Intracranial tumor	16823260	CNVD
Medulloblastoma	18056178	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Colorectal cancer	16272173	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Neuroblastoma	21899760	CNVD
Bladder cancer	19088036	CNVD
Ovarian neoplasms	16753589	CNVD
Glioblastoma multiforme	17002787	CNVD
Breast cancer	21858162	CNVD
Retinoblastoma	19183342	CNVD
Non-small cell lung cancer	21385341	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
Breast cancer	16608533	CNVD
Ewing''s sarcoma	22429812	CNVD
Acute promyelocytic leukemia	19109227	CNVD
Chordoma	18071362	CNVD
Hepatocellular carcinoma	18803288	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	17001317	CNVD
Urothelial carcinoma	21177765	CNVD
Burkitt''s lymphoma	19759907	CNVD
Acute myeloid leukemia	21251322	CNVD
Multiple myeloma	17550852	CNVD
Prostate cancer	18632612	CNVD
Acute myeloid leukemia	20729466	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Testicular germ cell tumor	18059402	CNVD
Trisomy 5 syndrome	21098271	CNVD
Ependymoma	18628472	CNVD
Leukemia	18628472	CNVD
Breast cancer	21611746	CNVD
Neuroblastoma	18923191	CNVD
Soft tissue tumor	16732325	CNVD
Cancer	17060936	CNVD
Lung cancer	16740712	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Ewing''s sarcoma	17952124	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
Acute lymphoblastic leukemia	19100363	CNVD
Williams-beuren syndrome	16971481	CNVD
Developmental delay	21147756	CNVD
Burkitt''s lymphoma	20823134	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Breast cancer	20409316	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Pancreatic cancer	17952125	CNVD
Myelofibrosis	22110671	CNVD
Breast cancer	21509527	CNVD

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171558800-171573200	Weak transcription	Small Intestine	intestine
2	chr1:171561200-171569800	Weak transcription	Pancreas	Pancrea
3	chr1:171561600-171570000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr1:171561600-171572200	Weak transcription	Aorta	Aorta
5	chr1:171561800-171570200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:171561800-171570200	Weak transcription	Lung	lung
7	chr1:171561800-171570400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr1:171561800-171572200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr1:171561800-171576600	Weak transcription	Brain Substantia Nigra	brain
10	chr1:171562000-171572000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr1:171562200-171571800	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr1:171562200-171575600	Weak transcription	HepG2	liver
13	chr1:171562800-171572000	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr1:171562800-171572200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr1:171563200-171572000	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr1:171564000-171572200	Weak transcription	Fetal Kidney	kidney
17	chr1:171564400-171570600	Weak transcription	Brain Cingulate Gyrus	brain
18	chr1:171564400-171572000	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr1:171564400-171573000	Weak transcription	Adipose Nuclei	Adipose
20	chr1:171564800-171570200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr1:171566200-171572000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr1:171569200-171576400	Weak transcription	GM12878-XiMat	blood
23	chr1:171569400-171570200	Enhancers	Liver	Liver
24	chr1:171569600-171570200	Weak transcription	Brain Anterior Caudate	brain
25	chr1:171570000-171570200	Enhancers	Pancreas	Pancrea
26	chr1:171570200-171570400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr1:171570200-171570400	Enhancers	Brain Anterior Caudate	brain
28	chr1:171570200-171570400	Enhancers	Lung	lung
29	chr1:171570200-171575600	Weak transcription	Liver	Liver
30	chr1:171570600-171570800	Enhancers	Brain Cingulate Gyrus	brain
31	chr1:171572000-171572200	Enhancers	HUES48 Cell Line	embryonic stem cell
32	chr1:171572000-171572400	Enhancers	ES-I3 Cell Line	embryonic stem cell
33	chr1:171572000-171572600	Enhancers	H1 Cell Line	embryonic stem cell
34	chr1:171572000-171572600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr1:171572000-171572600	Enhancers	HUES6 Cell Line	embryonic stem cell
36	chr1:171572000-171572600	Enhancers	HUES64 Cell Line	embryonic stem cell
37	chr1:171572200-171572400	Enhancers	H9 Cell Line	embryonic stem cell
38	chr1:171572200-171572400	Enhancers	iPS-18 Cell Line	embryonic stem cell
39	chr1:171572200-171572400	Enhancers	Aorta	Aorta
40	chr1:171572200-171572400	Enhancers	Fetal Kidney	kidney
41	chr1:171572200-171572600	Enhancers	iPS-15b Cell Line	embryonic stem cell
42	chr1:171573000-171573200	Enhancers	Adipose Nuclei	Adipose
43	chr1:171573200-171573400	Enhancers	Small Intestine	intestine
44	chr1:171573200-171579600	Weak transcription	Adipose Nuclei	Adipose
45	chr1:171575600-171576000	Enhancers	Liver	Liver
46	chr1:171575600-171576000	Enhancers	HepG2	liver

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