Variant report

Variant	nsv460556
Chromosome Location	chr3:54270646-54293345
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	chr3:54286387..54287180-chr8:129442741..129443555,2	MCF-7	breast:

Extended variants
information (count: 1005 )
Associated
traits (count: 91 )

Variant overlapped rSNPs/rCNVs (count:1005 , 50 per page) page: 1 2 3 4 5 6 7 ... 21

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs11130405	chr3:54270646-54270647	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs11916400	chr3:54270693-54270694	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs139596332	chr3:54270694-54270695	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs536670248	chr3:54270708-54270709	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs184409551	chr3:54270722-54270723	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs570126088	chr3:54270728-54270729	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs539141515	chr3:54270734-54270735	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs557643311	chr3:54270746-54270747	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs145123697	chr3:54270748-54270749	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs562099222	chr3:54270750-54270751	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs9839160	chr3:54270833-54270834	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
12	rs533830303	chr3:54270887-54270888	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs79393706	chr3:54270897-54270898	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs373883819	chr3:54270903-54270904	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs554063850	chr3:54270905-54270906	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs147942875	chr3:54270906-54270907	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs542256899	chr3:54271008-54271009	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs555748213	chr3:54271026-54271027	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs201978347	chr3:54271035-54271036	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs575683607	chr3:54271038-54271039	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs74553858	chr3:54271049-54271050	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs544725027	chr3:54271061-54271062	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs565302329	chr3:54271065-54271066	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs189700981	chr3:54271160-54271161	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs116537638	chr3:54271161-54271162	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs181157494	chr3:54271179-54271180	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs530106268	chr3:54271195-54271196	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs550154674	chr3:54271374-54271375	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs77804871	chr3:54271424-54271425	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs530996599	chr3:54271485-54271486	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs143823781	chr3:54271518-54271519	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs549297662	chr3:54271522-54271523	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs151107413	chr3:54271541-54271542	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs571334450	chr3:54271561-54271562	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs534043256	chr3:54271582-54271583	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs553775222	chr3:54271634-54271635	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs567181293	chr3:54271662-54271663	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs76330145	chr3:54271666-54271667	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs375891671	chr3:54271686-54271687	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs555709450	chr3:54271701-54271702	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs186151281	chr3:54271737-54271738	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs544688185	chr3:54271743-54271744	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs114345480	chr3:54271745-54271746	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs111979530	chr3:54271763-54271764	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs555078518	chr3:54271771-54271772	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs116231458	chr3:54271778-54271779	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs115577182	chr3:54271791-54271792	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs561327930	chr3:54271829-54271830	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs553085922	chr3:54271848-54271849	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs530391704	chr3:54271871-54271872	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:91)

Disease	PMID	Source
Acute myeloid leukemia	20729466	CNVD
Urothelial carcinoma	18382360	CNVD
Melanoma	18172304	CNVD
Cervical cancer	21062161	CNVD
Hirschsprung''s Disease	21712996	CNVD
Glioblastoma multiforme	21080181	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Insulin resistance	16721378	CNVD
Neuroblastoma	18664255	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Multiple myeloma	17077331	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Ewing''s sarcoma	21437220	CNVD
Neuroblastoma	21484798	CNVD
Non-small cell lung cancer	21044232	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Oral cancer	19627613	CNVD
Renal cell carcinoma	19461508	CNVD
Epithelial cancer	22065749	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Acute myeloid leukemia	16864856	CNVD
Liposarcoma	21253554	CNVD
Basal cell lymphoma	21115979	CNVD
Endometrial cancer	22040021	CNVD
Pancreatic endocrine tumor	20981439	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	17387387	CNVD
Oral cancer	21386901	CNVD
Cutaneous squamous cell carcinomas	19131950	CNVD
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Retinoblastoma	21504564	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Renal cell carcinoma	21668985	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Lung cancer	18438408	CNVD
Intellectual disability	22102821	CNVD
Breast cancer	17603634	CNVD
Esophageal cancer	20955586	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Breast cancer	17133270	CNVD
Uveal melanoma	20484589	CNVD
Autism	22495311	CNVD
Melanoma	20688739	CNVD
Acute myeloid leukemia	21251322	CNVD
Hepatocellular carcinoma	16750200	CNVD
Cancer	21183584	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Bipolar disorder	20877625	CNVD
Bipolar disorder	21956041	CNVD
Bipolar disorder	22241247	CNVD
Biliary cancer	18923514	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Malignant mesothelioma	18160781	CNVD
Pleural malignant mesothelioma	18160781	CNVD
Breast cancer	16397240	CNVD
Breast cancer	22032731	CNVD
Non-small cell lung cancer	20864512	CNVD
Colorectal cancer	16912164	CNVD
Non-small cell lung cancer	19010865	CNVD
Colorectal cancer	16272173	CNVD
Non-muscle invasive bladder neoplasm	19445696	CNVD
Breast cancer	21785460	CNVD
Neuroblastoma	17327916	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Septo-optic dysplasia	21572526	CNVD
Biliary cancer	19435499	CNVD
Squamous cell cancer	20885788	CNVD
Myelofibrosis	22110671	CNVD
Urothelial cell carcinoma	18451213	CNVD
Ventriculomegaly	21325761	CNVD
Breast cancer	16608533	CNVD
Prostate cancer	21965145	CNVD
Cancer	21129771	CNVD
Congenital diaphragmatic hernia	21085971	CNVD
Lung cancer	16618734	CNVD
Neuroblastoma	19686582	CNVD
Renal cell carcinoma	18765545	CNVD
small cell lung cancer	20016488	CNVD
Pancreatic ductal adenocarcinoma	19077451	CNVD
Breast cancer	21509527	CNVD
Prostate cancer	18632612	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54260400-54271200	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr3:54265200-54279600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:54265400-54278000	Weak transcription	Psoas Muscle	Psoas
4	chr3:54270000-54270800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:54270000-54271200	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr3:54270400-54274400	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr3:54270800-54271400	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr3:54270800-54271800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr3:54271200-54271400	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr3:54271800-54272400	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr3:54271800-54273600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr3:54272200-54275600	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr3:54272400-54272800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr3:54272800-54273000	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr3:54273000-54274400	Enhancers	Brain Germinal Matrix	brain
16	chr3:54273000-54277800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr3:54273600-54274600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr3:54274200-54274800	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr3:54274400-54274800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
20	chr3:54274400-54274800	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr3:54275400-54275800	Enhancers	Right Atrium	heart
22	chr3:54275600-54276000	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr3:54275800-54277000	Weak transcription	Right Atrium	heart
24	chr3:54276000-54277000	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr3:54276600-54277000	Enhancers	Ovary	ovary
26	chr3:54276600-54278000	Active TSS	Brain Angular Gyrus	brain
27	chr3:54276800-54277000	Enhancers	Brain Inferior Temporal Lobe	brain
28	chr3:54276800-54277000	Enhancers	Fetal Lung	lung
29	chr3:54276800-54278200	Enhancers	Fetal Brain Male	brain
30	chr3:54277000-54277200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr3:54277000-54277200	Flanking Active TSS	Ovary	ovary
32	chr3:54277000-54277400	Flanking Active TSS	Fetal Lung	lung
33	chr3:54277000-54277400	Flanking Active TSS	Right Atrium	heart
34	chr3:54277000-54277400	Enhancers	Spleen	Spleen
35	chr3:54277000-54277600	Active TSS	Stomach Smooth Muscle	stomach
36	chr3:54277000-54277600	Flanking Bivalent TSS/Enh	HepG2	liver
37	chr3:54277000-54277800	Active TSS	Brain Anterior Caudate	brain
38	chr3:54277000-54277800	Active TSS	Brain Cingulate Gyrus	brain
39	chr3:54277000-54277800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
40	chr3:54277000-54278000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr3:54277000-54278000	Active TSS	Muscle Satellite Cultured Cells	--
42	chr3:54277000-54278000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr3:54277000-54278000	Active TSS	Brain Hippocampus Middle	brain
44	chr3:54277000-54278000	Active TSS	Brain Inferior Temporal Lobe	brain
45	chr3:54277000-54278000	Active TSS	Duodenum Mucosa	Duodenum
46	chr3:54277000-54278000	Active TSS	Skeletal Muscle Male	skeletal muscle
47	chr3:54277000-54278000	Active TSS	Skeletal Muscle Female	skeletal muscle
48	chr3:54277000-54278000	Active TSS	A549	lung
49	chr3:54277000-54278200	Active TSS	NHLF	lung
50	chr3:54277200-54277400	Bivalent Enhancer	Fetal Stomach	stomach

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