Variant report

Variant	esv1828457
Chromosome Location	chr3:28193856-28207763
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:28192472..28194097-chr3:28198773..28201544,2	K562	blood:
2	chr3:28196891..28198936-chr3:28200402..28202674,2	K562	blood:
3	chr3:28194249..28196300-chr3:28389824..28392294,2	K562	blood:
4	chr3:28206434..28209003-chr3:28281528..28284368,2	K562	blood:
5	chr3:28192472..28194097-chr3:28198773..28201544,2	K562	blood:
6	chr3:28196891..28198936-chr3:28200402..28202674,2	K562	blood:

Variant related genes	Relation type
ENSG00000206559	chromatin interactions
ENSG00000187118	chromatin interactions
ENSG00000163512	chromatin interactions

Extended variants
information (count: 233 )
Associated
traits (count: 72 )

Variant overlapped rSNPs/rCNVs (count:233 , 50 per page) page: 1 2 3 4 5

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs925527	chr3:28193856-28193857	Flanking Active TSS Active TSS Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs114442957	chr3:28193860-28193861	Flanking Active TSS Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs575702481	chr3:28193861-28193862	Flanking Active TSS Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs544661169	chr3:28193866-28193867	Flanking Active TSS Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs564547730	chr3:28193929-28193930	Flanking Active TSS Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs578072163	chr3:28193931-28193932	Flanking Active TSS Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs2172437	chr3:28193977-28193978	Flanking Active TSS Active TSS Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
8	rs560706653	chr3:28193980-28193981	Flanking Active TSS Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs373754975	chr3:28194055-28194056	Enhancers Active TSS Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
10	rs552840143	chr3:28194144-28194145	Enhancers Active TSS Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
11	rs2131447	chr3:28194182-28194183	Enhancers Active TSS Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
12	rs562883918	chr3:28194252-28194253	Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
13	rs531186123	chr3:28194310-28194311	Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
14	rs141631732	chr3:28194337-28194338	Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
15	rs557537496	chr3:28194357-28194358	Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
16	rs112290654	chr3:28194361-28194362	Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
17	rs183879702	chr3:28194385-28194386	Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
18	rs533858236	chr3:28194396-28194397	Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
19	rs188252962	chr3:28194441-28194442	Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
20	rs150508926	chr3:28194515-28194516	Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
21	rs536494711	chr3:28194529-28194530	Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
22	rs112138540	chr3:28194534-28194535	Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
23	rs576430449	chr3:28194565-28194566	Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
24	rs528842882	chr3:28194649-28194650	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
25	rs141835114	chr3:28194653-28194654	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
26	rs548854255	chr3:28194707-28194708	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
27	rs557063159	chr3:28194731-28194732	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
28	rs568057636	chr3:28194765-28194766	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
29	rs540674729	chr3:28194772-28194773	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
30	rs373594916	chr3:28194814-28194815	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
31	rs200422033	chr3:28194865-28194866	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
32	rs551068984	chr3:28194892-28194893	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
33	rs560391307	chr3:28194897-28194898	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
34	rs146252062	chr3:28194956-28194957	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
35	rs367770203	chr3:28194963-28194964	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
36	rs550527932	chr3:28194973-28194974	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
37	rs531851039	chr3:28194997-28194998	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
38	rs551679859	chr3:28195017-28195018	ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
39	rs564852453	chr3:28195026-28195027	ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
40	rs370229012	chr3:28195058-28195059	ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
41	rs527301121	chr3:28195060-28195061	ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
42	rs547462798	chr3:28195068-28195069	ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
43	rs570486227	chr3:28195117-28195118	ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
44	rs139330000	chr3:28195160-28195161	ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
45	rs536426876	chr3:28195161-28195162	ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
46	rs191210774	chr3:28195219-28195220	ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
47	rs115629444	chr3:28195223-28195224	ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
48	rs77420680	chr3:28195236-28195237	ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
49	rs532698053	chr3:28195259-28195260	ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
50	rs149922559	chr3:28195300-28195301	ZNF genes & repeats	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:72)

Disease	PMID	Source
Chronic lymphocytic leukemia	21546498	CNVD
Breast cancer	17603634	CNVD
Neuroblastoma	17327916	CNVD
Glioblastoma multiforme	21080181	CNVD
Neuroblastoma	18923191	CNVD
Colorectal cancer	21297112	CNVD
Lynch syndrome	18415027	CNVD
Renal cell carcinoma	18592004	CNVD
Acute myeloid leukemia	20729466	CNVD
Urothelial carcinoma	18382360	CNVD
Melanoma	18172304	CNVD
Cervical cancer	21062161	CNVD
Hirschsprung''s Disease	21712996	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
lymphocytic leukemia	21291569	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Renal cell carcinoma	21668985	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Lung cancer	20668451	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Intellectual disability	22102821	CNVD
Esophageal cancer	20955586	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Squamous cell cancer	20885788	CNVD
Breast cancer	17133270	CNVD
Uveal melanoma	20484589	CNVD
Autism	22495311	CNVD
Melanoma	20688739	CNVD
Acute myeloid leukemia	21251322	CNVD
Myelofibrosis	22110671	CNVD
Lung cancer	16618734	CNVD
Cancer	20164919	CNVD
Developmental delay	21147756	CNVD

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:28192400-28194000	Enhancers	Primary T helper cells PMA-I stimulated	--
2	chr3:28192600-28194000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr3:28192600-28194200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr3:28192600-28194200	Enhancers	Primary T helper cells fromperipheralblood	blood
5	chr3:28192600-28194200	Enhancers	Small Intestine	intestine
6	chr3:28193200-28194000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr3:28193200-28194000	Active TSS	GM12878-XiMat	blood
8	chr3:28193200-28194200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr3:28193200-28194200	Enhancers	Primary T killer memory cells from peripheral blood	blood
10	chr3:28193200-28194200	Flanking Active TSS	Dnd41	blood
11	chr3:28193600-28194000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr3:28193600-28194000	Active TSS	Duodenum Smooth Muscle	Duodenum
13	chr3:28193600-28194200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr3:28193600-28194200	Enhancers	Primary T helper naive cells from peripheral blood	blood
15	chr3:28193800-28194200	Enhancers	Adipose Nuclei	Adipose
16	chr3:28193800-28194200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr3:28194000-28194200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr3:28194000-28194200	Enhancers	Sigmoid Colon	Sigmoid Colon
19	chr3:28194200-28194600	Enhancers	Dnd41	blood
20	chr3:28194600-28195000	Weak transcription	Dnd41	blood
21	chr3:28194800-28195000	Weak transcription	Liver	Liver
22	chr3:28195000-28195400	ZNF genes & repeats	Dnd41	blood
23	chr3:28196600-28197200	Enhancers	Fetal Brain Female	brain
24	chr3:28196800-28198200	Enhancers	Fetal Brain Male	brain
25	chr3:28198600-28199200	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr3:28198800-28199200	Enhancers	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links