Variant report

Variant	esv3361292
Chromosome Location	chr3:53850372-53850895
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	chr3:53849527..53851449-chr3:53878802..53881652,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000056736	chromatin interactions
ENSG00000016391	chromatin interactions

Extended variants
information (count: 22 )
Associated
traits (count: 92 )

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs187834555	chr3:53850417-53850418	Weak transcription Strong transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
2	rs554131598	chr3:53850427-53850428	Weak transcription Strong transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs192184790	chr3:53850462-53850463	Weak transcription Strong transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
4	rs4234642	chr3:53850475-53850476	Weak transcription Strong transcription Enhancers	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
5	rs139666092	chr3:53850532-53850533	Weak transcription Strong transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
6	rs554953502	chr3:53850544-53850545	Weak transcription Strong transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
7	rs74840452	chr3:53850571-53850572	Weak transcription Strong transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
8	rs543655401	chr3:53850592-53850593	Weak transcription Strong transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
9	rs563875458	chr3:53850658-53850659	Weak transcription Strong transcription Enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
10	rs530025974	chr3:53850687-53850688	Weak transcription Strong transcription Enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
11	rs149740306	chr3:53850724-53850725	Weak transcription Strong transcription Enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs544684173	chr3:53850725-53850726	Weak transcription Strong transcription Enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
13	rs184612853	chr3:53850757-53850758	Weak transcription Strong transcription Enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
14	rs558250205	chr3:53850774-53850775	Weak transcription Strong transcription Enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
15	rs547329133	chr3:53850780-53850781	Weak transcription Strong transcription Enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
16	rs374540464	chr3:53850784-53850785	Weak transcription Strong transcription Enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
17	rs376877839	chr3:53850811-53850812	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
18	rs4563403	chr3:53850814-53850815	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
19	rs529972455	chr3:53850815-53850816	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
20	rs144461528	chr3:53850843-53850844	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
21	rs11714712	chr3:53850855-53850856	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
22	rs3079411	chr3:53850868-53850869	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	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
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
Chronic lymphocytic leukemia	20421269	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
Breast cancer	21509527	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53829200-53853000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:53830400-53851200	Weak transcription	Fetal Brain Male	brain
3	chr3:53839200-53855200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr3:53839400-53851400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr3:53839600-53851000	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr3:53839600-53851200	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr3:53839600-53852800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr3:53839600-53876600	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr3:53840600-53851200	Weak transcription	Aorta	Aorta
10	chr3:53840800-53853600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr3:53841000-53852600	Weak transcription	Ovary	ovary
12	chr3:53841000-53852800	Weak transcription	Stomach Smooth Muscle	stomach
13	chr3:53841400-53850400	Weak transcription	Brain Hippocampus Middle	brain
14	chr3:53841600-53851000	Weak transcription	Brain Angular Gyrus	brain
15	chr3:53841600-53851200	Weak transcription	Colonic Mucosa	Colon
16	chr3:53841600-53851400	Weak transcription	Fetal Muscle Leg	muscle
17	chr3:53841600-53851400	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr3:53841600-53855600	Weak transcription	Right Ventricle	heart
19	chr3:53841600-53855800	Weak transcription	Right Atrium	heart
20	chr3:53841800-53850600	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr3:53841800-53850600	Weak transcription	HepG2	liver
22	chr3:53841800-53851200	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr3:53841800-53853400	Weak transcription	Fetal Brain Female	brain
24	chr3:53841800-53853400	Weak transcription	GM12878-XiMat	blood
25	chr3:53842200-53852200	Strong transcription	Fetal Intestine Small	intestine
26	chr3:53842200-53852600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr3:53842200-53857200	Strong transcription	Fetal Intestine Large	intestine
28	chr3:53842400-53855600	Weak transcription	Fetal Heart	heart
29	chr3:53844400-53852000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr3:53844600-53851200	Weak transcription	Spleen	Spleen
31	chr3:53845400-53850800	Weak transcription	Gastric	stomach
32	chr3:53846200-53850800	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr3:53846600-53879800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr3:53846800-53851200	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr3:53847000-53856400	Weak transcription	Brain Germinal Matrix	brain
36	chr3:53847000-53862000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr3:53847600-53852200	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr3:53848200-53851800	Weak transcription	Esophagus	oesophagus
39	chr3:53849000-53857200	Strong transcription	Duodenum Mucosa	Duodenum
40	chr3:53849000-53857800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr3:53849000-53858200	Strong transcription	Fetal Stomach	stomach
42	chr3:53849000-53858800	Strong transcription	Liver	Liver
43	chr3:53849000-53859200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr3:53849000-53866800	Weak transcription	Stomach Mucosa	stomach
45	chr3:53849200-53850600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr3:53849200-53852000	Enhancers	Cortex derived primary cultured neurospheres	brain
47	chr3:53849200-53853800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr3:53849400-53851600	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr3:53849400-53851600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr3:53849600-53851400	Weak transcription	H9 Cell Line	embryonic stem cell

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