Variant report

Variant	esv3463346
Chromosome Location	chr3:52210322-52210752
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:52006199..52007889-chr3:52209078..52210620,2	K562	blood:
2	chr3:52209128..52211243-chr3:52227235..52228874,2	MCF-7	breast:
3	chr3:52208921..52211752-chr3:52239089..52241335,2	MCF-7	breast:
4	chr3:52209175..52211275-chr3:52220260..52222070,2	K562	blood:
5	chr3:52205965..52208673-chr3:52209831..52213095,4	K562	blood:
6	chr3:52206232..52208818-chr3:52209949..52213336,4	K562	blood:

Variant related genes	Relation type
ENSG00000023330	chromatin interactions
ENSG00000248487	chromatin interactions

Extended variants
information (count: 18 )
Associated
traits (count: 89 )

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs542878258	chr3:52210346-52210347	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
2	rs561055288	chr3:52210373-52210374	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs371716063	chr3:52210385-52210386	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
4	rs11335572	chr3:52210411-52210412	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
5	rs531481913	chr3:52210420-52210421	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
6	rs369729024	chr3:52210458-52210459	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
7	rs549852632	chr3:52210462-52210463	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
8	rs60640965	chr3:52210532-52210533	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
9	rs75418800	chr3:52210564-52210565	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
10	rs532154664	chr3:52210580-52210581	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
11	rs562751468	chr3:52210589-52210590	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs547055650	chr3:52210592-52210593	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
13	rs145897003	chr3:52210649-52210650	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs534210361	chr3:52210656-52210657	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs352152	chr3:52210700-52210701	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
16	rs185867711	chr3:52210719-52210720	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs368966091	chr3:52210748-52210749	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs145192672	chr3:52210749-52210750	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:89)

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
small cell lung cancer	20016488	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
Bladder cancer	21909424	CNVD
Chronic lymphocytic leukemia	20421269	CNVD
Septo-optic dysplasia	21572526	CNVD
Biliary cancer	19435499	CNVD
Squamous cell cancer	20885788	CNVD
Pancreatic ductal adenocarcinoma	19077451	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
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52196200-52210400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr3:52204800-52215600	Weak transcription	Right Ventricle	heart
3	chr3:52206000-52211000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr3:52206200-52210400	Weak transcription	Gastric	stomach
5	chr3:52206200-52210600	Weak transcription	Stomach Mucosa	stomach
6	chr3:52207600-52210400	Weak transcription	Adipose Nuclei	Adipose
7	chr3:52208400-52212800	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr3:52209000-52210600	Weak transcription	NHEK	skin
9	chr3:52209000-52211000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr3:52209200-52211000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr3:52209200-52211000	Weak transcription	HMEC	breast
12	chr3:52209200-52211000	Weak transcription	NHLF	lung
13	chr3:52209200-52212000	Enhancers	Spleen	Spleen
14	chr3:52209400-52210600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr3:52209400-52210600	Weak transcription	Hela-S3	cervix
16	chr3:52209400-52211200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr3:52209600-52210600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr3:52209800-52211600	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr3:52210000-52210400	Enhancers	HepG2	liver
20	chr3:52210000-52211000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr3:52210000-52212200	Enhancers	Esophagus	oesophagus
22	chr3:52210000-52218200	Enhancers	Liver	Liver
23	chr3:52210200-52213200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr3:52210400-52210800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr3:52210400-52211600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr3:52210400-52212000	Enhancers	Gastric	stomach
27	chr3:52210400-52212200	Enhancers	Adipose Nuclei	Adipose
28	chr3:52210400-52212200	Flanking Active TSS	HepG2	liver
29	chr3:52210400-52213200	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr3:52210600-52210800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr3:52210600-52210800	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr3:52210600-52210800	Enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr3:52210600-52210800	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
34	chr3:52210600-52210800	Flanking Active TSS	Hela-S3	cervix
35	chr3:52210600-52211400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr3:52210600-52211600	Enhancers	Lung	lung
37	chr3:52210600-52211600	Enhancers	NHEK	skin
38	chr3:52210600-52212000	Enhancers	Stomach Mucosa	stomach
39	chr3:52210600-52212600	Enhancers	Fetal Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links