Variant report

Variant	esv3434928
Chromosome Location	chr3:53550812-53554010
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:53553135..53554029-chr3:53584915..53585873,10	MCF-7	breast:
2	chr3:53552367..53553946-chr3:53584985..53585902,8	MCF-7	breast:
3	chr3:53552361..53552892-chr3:53585085..53585894,2	MCF-7	breast:
4	chr3:53553264..53553901-chr3:53741724..53742273,2	MCF-7	breast:
5	chr3:53552361..53553110-chr3:53585085..53585894,4	MCF-7	breast:
6	chr3:53553135..53553983-chr3:53584999..53585589,3	MCF-7	breast:
7	chr3:53552476..53553069-chr3:53585002..53585791,2	MCF-7	breast:

Extended variants
information (count: 113 )
Associated
traits (count: 92 )

Variant overlapped rSNPs/rCNVs (count:113 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs573111522	chr3:53550816-53550817	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs191572621	chr3:53550819-53550820	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs143069621	chr3:53550909-53550910	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs575046156	chr3:53551009-53551010	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs3774421	chr3:53551010-53551011	Weak transcription Strong transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
6	rs183822603	chr3:53551018-53551019	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs533248381	chr3:53551019-53551020	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs540646235	chr3:53551029-53551030	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs560254614	chr3:53551083-53551084	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs186795846	chr3:53551120-53551121	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs147406126	chr3:53551141-53551142	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs9840426	chr3:53551142-53551143	Weak transcription Strong transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
13	rs79420186	chr3:53551154-53551155	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs555247714	chr3:53551165-53551166	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs11274777	chr3:53551222-53551223	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs149127883	chr3:53551246-53551247	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs145910659	chr3:53551247-53551248	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs375381178	chr3:53551249-53551250	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs376302024	chr3:53551255-53551256	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs551666585	chr3:53551267-53551268	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs34951656	chr3:53551346-53551347	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs570553974	chr3:53551357-53551358	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs554556685	chr3:53551370-53551371	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs190707432	chr3:53551390-53551391	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs368270963	chr3:53551438-53551439	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs552946891	chr3:53551450-53551451	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs139714058	chr3:53551451-53551452	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs146032040	chr3:53551502-53551503	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs535362546	chr3:53551507-53551508	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs529370207	chr3:53551515-53551516	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs555286363	chr3:53551518-53551519	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs575177478	chr3:53551519-53551520	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs183358364	chr3:53551526-53551527	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs186531537	chr3:53551570-53551571	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs79853140	chr3:53551575-53551576	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs147225916	chr3:53551646-53551647	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs560544258	chr3:53551659-53551660	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs574130117	chr3:53551682-53551683	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs543033455	chr3:53551700-53551701	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs563207515	chr3:53551723-53551724	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs532021402	chr3:53551737-53551738	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs113835384	chr3:53551753-53551754	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs568223206	chr3:53551769-53551770	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs565300190	chr3:53551798-53551799	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs533053237	chr3:53551804-53551805	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs116084360	chr3:53551805-53551806	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs72957271	chr3:53551817-53551818	Weak transcription Enhancers Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
48	rs112886145	chr3:53551834-53551835	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs548550171	chr3:53551868-53551869	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs312481	chr3:53551902-53551903	Weak transcription Enhancers Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a

Variant related diseases (count:92)

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
Prostate cancer	18632612	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
Chronic lymphocytic leukemia	20421269	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
Adrenocortical carcinoma	18281524	CNVD
small cell lung cancer	20016488	CNVD
Pancreatic ductal adenocarcinoma	19077451	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53533600-53552000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr3:53540600-53552200	Weak transcription	Spleen	Spleen
3	chr3:53540600-53560000	Weak transcription	Pancreas	Pancrea
4	chr3:53542600-53551400	Strong transcription	Fetal Intestine Large	intestine
5	chr3:53545200-53552800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr3:53545400-53552800	Weak transcription	Fetal Stomach	stomach
7	chr3:53545600-53551200	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr3:53545600-53552000	Weak transcription	Lung	lung
9	chr3:53547200-53553200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:53548200-53552200	Strong transcription	Fetal Intestine Small	intestine
11	chr3:53550000-53552000	Enhancers	A549	lung
12	chr3:53550600-53551400	Strong transcription	Fetal Lung	lung
13	chr3:53550800-53552000	Enhancers	Hela-S3	cervix
14	chr3:53551200-53551400	Enhancers	Brain Hippocampus Middle	brain
15	chr3:53551200-53551400	Enhancers	Brain Inferior Temporal Lobe	brain
16	chr3:53551200-53552400	Enhancers	Monocytes-CD14+_RO01746	blood
17	chr3:53551200-53553000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr3:53551200-53554400	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr3:53551400-53551800	Weak transcription	Fetal Lung	lung
20	chr3:53551400-53552000	Weak transcription	Fetal Intestine Large	intestine
21	chr3:53551400-53559000	Weak transcription	Brain Hippocampus Middle	brain
22	chr3:53551400-53559800	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr3:53551800-53552600	Enhancers	Fetal Lung	lung
24	chr3:53552000-53552600	Enhancers	Fetal Intestine Large	intestine
25	chr3:53552000-53552600	Enhancers	Lung	lung
26	chr3:53552000-53552600	Flanking Active TSS	A549	lung
27	chr3:53552000-53553000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr3:53552000-53553600	Enhancers	Placenta	Placenta
29	chr3:53552000-53554000	Enhancers	Duodenum Smooth Muscle	Duodenum
30	chr3:53552000-53554000	Flanking Active TSS	Hela-S3	cervix
31	chr3:53552000-53554400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr3:53552200-53552400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
33	chr3:53552200-53552400	Enhancers	Stomach Mucosa	stomach
34	chr3:53552200-53553200	Enhancers	Liver	Liver
35	chr3:53552200-53553200	Enhancers	Brain Anterior Caudate	brain
36	chr3:53552200-53553200	Enhancers	Spleen	Spleen
37	chr3:53552200-53555000	Weak transcription	Fetal Intestine Small	intestine
38	chr3:53552400-53553200	Enhancers	Ovary	ovary
39	chr3:53552400-53553600	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr3:53552400-53553600	Enhancers	Primary neutrophils fromperipheralblood	blood
41	chr3:53552400-53554000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
42	chr3:53552400-53568400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr3:53552600-53553200	Flanking Active TSS	Fetal Lung	lung
44	chr3:53552600-53553400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr3:53552600-53553400	Enhancers	Colon Smooth Muscle	Colon
46	chr3:53552600-53553400	Genic enhancers	Fetal Intestine Large	intestine
47	chr3:53552600-53553400	Active TSS	A549	lung
48	chr3:53552600-53560200	Weak transcription	Lung	lung
49	chr3:53552800-53553400	Enhancers	Pancreatic Islets	Pancreatic Islet
50	chr3:53552800-53553400	Enhancers	Fetal Stomach	stomach

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