Variant report

Variant	esv3474352
Chromosome Location	chr6:161215481-161218806
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	chr6:161213757..161216214-chr6:161411268..161413950,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LPA-1	chr6:161216349-161216488	XLOC_005905

Variant related genes	Relation type
ENSG00000085511	chromatin interactions
ENSG00000272841	chromatin interactions

Extended variants
information (count: 78 )
Associated
traits (count: 82 )

Variant overlapped rSNPs/rCNVs (count:78 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs192079516	chr6:161215488-161215489	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
2	rs549679105	chr6:161215516-161215517	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs566360921	chr6:161215537-161215538	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
4	rs76200625	chr6:161215538-161215539	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
5	rs551796188	chr6:161215561-161215562	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
6	rs369520835	chr6:161215564-161215565	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
7	rs113389682	chr6:161215570-161215571	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
8	rs537510756	chr6:161215619-161215620	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
9	rs529236703	chr6:161215641-161215642	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
10	rs556098701	chr6:161215662-161215663	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
11	rs538516251	chr6:161215672-161215673	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs183006679	chr6:161215728-161215729	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
13	rs75796333	chr6:161215756-161215757	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
14	rs373832439	chr6:161215790-161215791	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
15	rs572049760	chr6:161215832-161215833	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
16	rs114090237	chr6:161215939-161215940	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
17	rs148539778	chr6:161215952-161215953	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
18	rs373769629	chr6:161215985-161215986	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
19	rs557291691	chr6:161216001-161216002	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
20	rs4709470	chr6:161216023-161216024	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
21	rs373582736	chr6:161216124-161216125	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
22	rs543477677	chr6:161216147-161216148	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
23	rs112350060	chr6:161216187-161216188	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
24	rs371889891	chr6:161216189-161216190	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
25	rs142780037	chr6:161216250-161216251	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs376177025	chr6:161216282-161216283	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs542842999	chr6:161216346-161216347	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs2115867	chr6:161216358-161216359	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
29	rs73784975	chr6:161216375-161216376	Enhancers Weak transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
30	rs528747127	chr6:161216376-161216377	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
31	rs376404373	chr6:161216378-161216379	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
32	rs368604043	chr6:161216430-161216431	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
33	rs74766826	chr6:161216437-161216438	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
34	rs571631373	chr6:161216438-161216439	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
35	rs559917029	chr6:161216451-161216452	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
36	rs530928997	chr6:161216453-161216454	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
37	rs549378374	chr6:161216455-161216456	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
38	rs529024869	chr6:161216501-161216502	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs551079247	chr6:161216561-161216562	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs112398533	chr6:161216571-161216572	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs535690923	chr6:161216591-161216592	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs568647054	chr6:161216607-161216608	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs2064712	chr6:161216608-161216609	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	mRNA abundance
44	rs565649215	chr6:161216610-161216611	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs73784976	chr6:161216624-161216625	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
46	rs557354742	chr6:161216647-161216648	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs531921697	chr6:161216690-161216691	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs192426911	chr6:161216694-161216695	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs551405314	chr6:161216698-161216699	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs571146806	chr6:161216727-161216728	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:82)

Disease	PMID	Source
Uveal melanoma	21693616	CNVD
Glioblastoma multiforme	21080181	CNVD
Biliary cancer	19435499	CNVD
Medulloblastoma	21979893	CNVD
Malaria	21533027	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Ewing''s sarcoma	17952124	CNVD
Biliary cancer	20360734	CNVD
Breast cancer	20360734	CNVD
Coronary artery disease	20360734	CNVD
Crohn''s disease	20360734	CNVD
Hypertension	20360734	CNVD
Rheumatoid arthritis	20360734	CNVD
Type 1 diabetes	20360734	CNVD
Type 2 diabetes	20360734	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Neuroblastoma	18923191	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Melanoma	18172304	CNVD
Cancer	21637783	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Follicular lymphoma	19010834	CNVD
Non-small cell lung cancer	21044232	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	19960244	CNVD
Hepatocellular carcinoma	22174799	CNVD
Phyllodes tumor	17334353	CNVD
Breast cancer	16608533	CNVD
Non-small cell lung cancer	21385341	CNVD
Prostate cancer	16705090	CNVD
Adenoid cystic carcinoma	17372589	CNVD
Colorectal cancer	16272173	CNVD
Ependymoma	16718352	CNVD
Gastric cancer	17908304	CNVD
High-proliferative meningiomas	17937814	CNVD
Intracranial tumor	16823260	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	16272173	CNVD
Wilms tumour	21544195	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Congenital diaphragmatic hernia	21085971	CNVD
Malignant melanoma	18718029	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
Breast cancer	21858162	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Breast cancer	17603634	CNVD
Developmental delay	19490664	CNVD
Burkitt''s lymphoma	18698080	CNVD
Neurodevelopmental disorder	22521361	CNVD
small cell lung cancer	20016488	CNVD
Adenoid cystic carcinoma	18698036	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Leukemia	18688285	CNVD
Renal cell carcinoma	18592004	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Prostate cancer	18632612	CNVD
Lung cancer	18438408	CNVD
Burkitt''s lymphoma	19759907	CNVD
Esophageal cancer	21851588	CNVD
T-cell acute lymphoblastic leukemia	18185524	CNVD
Breast cancer	17133270	CNVD
Testicular germ cell tumor	18059402	CNVD
Developmental delay	21147756	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Chordoma	18071362	CNVD
Breast cancer	21509527	CNVD
Myelofibrosis	22110671	CNVD
Autism	22241247	CNVD
Breast cancer	16397240	CNVD
Atherosclerosis	21956041	CNVD
Maculopathy	20981449	CNVD
Retinoblastoma	22278416	CNVD
Primary central nervous system lymphoma	21088137	CNVD
Ovarian cancer	20844748	CNVD
Uveal melanoma	20484589	CNVD
Glioblastoma multiforme	19435819	CNVD
Astrocytoma	16205629	CNVD
Parkinson disease	17160897	CNVD

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:161211600-161216400	Weak transcription	Esophagus	oesophagus
2	chr6:161211600-161216400	Weak transcription	Placenta	Placenta
3	chr6:161214000-161216200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:161214000-161216800	Weak transcription	HMEC	breast
5	chr6:161214200-161215800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr6:161214600-161217200	Enhancers	NHEK	skin
7	chr6:161214600-161217600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr6:161214800-161217200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr6:161216200-161216400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr6:161216400-161216600	Enhancers	Placenta	Placenta
11	chr6:161216400-161216800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr6:161216400-161217200	Enhancers	Esophagus	oesophagus
13	chr6:161216800-161217200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr6:161216800-161217200	Enhancers	HMEC	breast

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