Variant report

Variant	esv3440427
Chromosome Location	chr3:55860016-55865704
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	chr3:55850876..55853376-chr3:55857822..55860534,2	MCF-7	breast:

Extended variants
information (count: 169 )
Associated
traits (count: 81 )

Variant overlapped rSNPs/rCNVs (count:169 , 50 per page) page: 1 2 3 4

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs549199159	chr3:55860030-55860031	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs544260157	chr3:55860043-55860044	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs564199258	chr3:55860076-55860077	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs111769475	chr3:55860109-55860110	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs546680244	chr3:55860110-55860111	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs183991428	chr3:55860198-55860199	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs188383304	chr3:55860213-55860214	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs548841497	chr3:55860238-55860239	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs79850770	chr3:55860288-55860289	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs181667019	chr3:55860350-55860351	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs550742522	chr3:55860371-55860372	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs536611287	chr3:55860376-55860377	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs570828177	chr3:55860380-55860381	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs138544701	chr3:55860391-55860392	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs553445864	chr3:55860424-55860425	Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs72877152	chr3:55860461-55860462	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
17	rs9874792	chr3:55860526-55860527	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
18	rs185853601	chr3:55860532-55860533	Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs150242796	chr3:55860557-55860558	Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs190736284	chr3:55860682-55860683	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs371021154	chr3:55860691-55860692	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs79132398	chr3:55860753-55860754	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs539916021	chr3:55860766-55860767	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs182022055	chr3:55860852-55860853	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs567189114	chr3:55860877-55860878	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs529036253	chr3:55860886-55860887	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs149371597	chr3:55860890-55860891	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs562435938	chr3:55860919-55860920	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs531452770	chr3:55860975-55860976	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs551663710	chr3:55861020-55861021	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
31	rs570722949	chr3:55861045-55861046	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
32	rs533384739	chr3:55861075-55861076	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
33	rs17714443	chr3:55861131-55861132	Enhancers Weak transcription Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
34	rs576319310	chr3:55861161-55861162	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
35	rs114257555	chr3:55861162-55861163	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
36	rs118131433	chr3:55861184-55861185	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
37	rs17056030	chr3:55861212-55861213	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
38	rs569478526	chr3:55861220-55861221	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
39	rs538117305	chr3:55861273-55861274	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
40	rs565912465	chr3:55861278-55861279	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
41	rs558242026	chr3:55861290-55861291	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
42	rs558444725	chr3:55861291-55861292	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
43	rs528360895	chr3:55861327-55861328	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
44	rs373943741	chr3:55861328-55861329	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
45	rs202247052	chr3:55861340-55861341	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
46	rs546239726	chr3:55861345-55861346	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
47	rs148957184	chr3:55861347-55861348	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
48	rs201537305	chr3:55861350-55861351	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
49	rs559653398	chr3:55861367-55861368	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
50	rs577541623	chr3:55861371-55861372	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:81)

Disease	PMID	Source
Melanoma	18172304	CNVD
Cervical cancer	21062161	CNVD
Hirschsprung''s Disease	21712996	CNVD
Acute myeloid leukemia	20729466	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
Myofibroblastic sarcoma	19369631	CNVD
Breast cancer	17133270	CNVD
Uveal melanoma	20484589	CNVD
Autism	22495311	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 mesothelioma	18160781	CNVD
Pleural malignant mesothelioma	18160781	CNVD
Non-muscle invasive bladder neoplasm	19445696	CNVD
Breast cancer	21785460	CNVD
Neuroblastoma	17327916	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Squamous cell cancer	20885788	CNVD
Breast cancer	16608533	CNVD
Prostate cancer	21965145	CNVD
Cancer	21129771	CNVD
Congenital diaphragmatic hernia	21085971	CNVD
Renal cell carcinoma	18765545	CNVD
small cell lung cancer	20016488	CNVD
Breast cancer	21509527	CNVD
Prostate cancer	18632612	CNVD
Cancer	20164919	CNVD
Myelofibrosis	22110671	CNVD
Urothelial cell carcinoma	18451213	CNVD
Breast cancer	19490591	CNVD
Autism	18414403	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Non-small cell lung cancer	20864512	CNVD
Metastatic melanoma	17975146	CNVD
Non-syndromic sensorineural hearing loss	21030649	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:55847600-55860200	Weak transcription	Fetal Lung	lung
2	chr3:55859800-55860400	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr3:55860000-55861800	Enhancers	Fetal Heart	heart
4	chr3:55860200-55862200	Enhancers	Fetal Lung	lung
5	chr3:55860400-55860600	Enhancers	Brain Inferior Temporal Lobe	brain
6	chr3:55860400-55861200	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr3:55860600-55861200	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr3:55860600-55861600	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr3:55860800-55861000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr3:55860800-55861200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr3:55860800-55861200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr3:55860800-55861200	Enhancers	Brain Germinal Matrix	brain
13	chr3:55860800-55861200	Enhancers	NH-A	brain
14	chr3:55861000-55861200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:55861000-55861200	Enhancers	Brain Hippocampus Middle	brain
16	chr3:55861000-55861200	Active TSS	Right Atrium	heart
17	chr3:55861000-55862200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr3:55861000-55862200	Active TSS	Brain Substantia Nigra	brain
19	chr3:55861200-55861800	Weak transcription	Brain Hippocampus Middle	brain
20	chr3:55861200-55863600	Weak transcription	Right Atrium	heart
21	chr3:55861400-55862400	Enhancers	Fetal Kidney	kidney
22	chr3:55861600-55861800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr3:55861600-55861800	Weak transcription	Brain Cingulate Gyrus	brain
24	chr3:55861600-55862000	Active TSS	Brain Anterior Caudate	brain
25	chr3:55861600-55862000	Enhancers	Brain Inferior Temporal Lobe	brain
26	chr3:55861800-55862200	Enhancers	Brain Cingulate Gyrus	brain
27	chr3:55861800-55862200	Active TSS	Brain Hippocampus Middle	brain
28	chr3:55862000-55862200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:55865200-55866000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:55865400-55865600	Enhancers	HUES6 Cell Line	embryonic stem cell
31	chr3:55865600-55866000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell

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