Variant report

Variant	nsv580958
Chromosome Location	chr2:9942159-9955047
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:68)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:68 , 50 per page) page: 1 2

No.	Distal block	Cell Line	Cell type
1	chr2:9947583..9953611-chr2:9980461..9984922,8	MCF-7	breast:
2	chr2:9953957..9955549-chr2:9981308..9984882,3	MCF-7	breast:
3	chr2:9941486..9944395-chr2:9967791..9970762,3	MCF-7	breast:
4	chr2:9945375..9947276-chr2:9949205..9951851,2	K562	blood:
5	chr2:9939689..9943559-chr2:10181776..10185625,4	K562	blood:
6	chr2:9953495..9955824-chr2:9964200..9966123,2	K562	blood:
7	chr2:9952171..9953849-chr2:9962646..9965376,2	MCF-7	breast:
8	chr2:9948192..9950621-chr2:10182726..10184931,3	MCF-7	breast:
9	chr2:9944322..9946964-chr2:10159875..10162614,2	MCF-7	breast:
10	chr2:9949069..9951498-chr2:10025282..10028550,3	MCF-7	breast:
11	chr2:9948913..9951655-chr2:9969307..9971290,2	MCF-7	breast:
12	chr2:9951629..9954793-chr2:10090886..10093950,3	MCF-7	breast:
13	chr2:9939670..9940467-chr2:9953617..9954536,3	K562	blood:
14	chr2:9948773..9949474-chr2:9970552..9971153,2	MCF-7	breast:
15	chr2:9953533..9955150-chr2:10188521..10190837,2	K562	blood:
16	chr2:9939487..9940276-chr2:9953657..9954192,2	MCF-7	breast:
17	chr2:9954114..9958283-chr2:10172857..10175994,4	K562	blood:
18	chr2:9951073..9955556-chr2:10089913..10091836,5	MCF-7	breast:
19	chr2:9941416..9943332-chr2:10258311..10260459,2	K562	blood:
20	chr2:9954879..9956876-chr2:9957733..9960340,3	K562	blood:
21	chr2:9945976..9947561-chr2:9982451..9984203,2	MCF-7	breast:
22	chr2:9945406..9947876-chr2:10182838..10184446,2	MCF-7	breast:
23	chr2:9953287..9954158-chr2:10212428..10212955,2	K562	blood:
24	chr2:9940003..9944697-chr2:9981835..9986230,10	MCF-7	breast:
25	chr2:9920939..9923701-chr2:9941195..9943026,2	MCF-7	breast:
26	chr2:9949625..9951614-chr2:9969038..9971229,2	MCF-7	breast:
27	chr2:9940167..9943661-chr2:10053697..10057580,3	MCF-7	breast:
28	chr2:9940648..9943036-chr2:10260275..10262065,2	K562	blood:
29	chr2:9940885..9945263-chr2:9946727..9949411,4	K562	blood:
30	chr2:9694708..9697029-chr2:9954430..9956483,2	MCF-7	breast:
31	chr2:9954341..9956671-chr2:9971127..9973681,2	K562	blood:
32	chr2:9941455..9943586-chr2:10099873..10102242,2	MCF-7	breast:
33	chr2:9953510..9955032-chr2:9983493..9985198,2	MCF-7	breast:
34	chr2:9955031..9957285-chr2:10091673..10093774,2	K562	blood:
35	chr2:9940189..9942989-chr2:10049056..10050927,2	MCF-7	breast:
36	chr2:9945041..9950358-chr2:10256783..10262735,6	K562	blood:
37	chr2:9908911..9912003-chr2:9940246..9943048,3	MCF-7	breast:
38	chr2:9940885..9945263-chr2:9946727..9949411,4	K562	blood:
39	chr2:9952585..9955462-chr2:9959911..9962016,2	MCF-7	breast:
40	chr2:9954254..9954818-chr8:59963704..59964295,2	MCF-7	breast:
41	chr2:9953452..9957551-chr2:10260663..10263596,3	K562	blood:
42	chr2:9945375..9947276-chr2:9949205..9951851,2	K562	blood:
43	chr2:9951674..9954142-chr2:10158863..10161812,2	MCF-7	breast:
44	chr2:9953775..9955121-chr2:10188515..10189751,8	K562	blood:
45	chr2:9954066..9954585-chr2:9970189..9971149,2	MCF-7	breast:
46	chr2:9938188..9943513-chr2:9981101..9985006,11	MCF-7	breast:
47	chr2:9942046..9945033-chr2:9945080..9947215,2	K562	blood:
48	chr2:9948978..9951882-chr2:10166549..10169090,2	MCF-7	breast:
49	chr2:9949012..9952005-chr2:9952060..9955056,3	K562	blood:
50	chr2:9954494..9957108-chr2:10173352..10175994,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000272524	chromatin interactions
ENSG00000151694	chromatin interactions
ENSG00000171848	chromatin interactions
ENSG00000271855	chromatin interactions
ENSG00000260476	chromatin interactions
ENSG00000115750	chromatin interactions
ENSG00000172059	chromatin interactions
ENSG00000260077	chromatin interactions
ENSG00000243491	chromatin interactions
ENSG00000134317	chromatin interactions

Extended variants
information (count: 583 )
Associated
traits (count: 60 )

Variant overlapped rSNPs/rCNVs (count:583 , 50 per page) page: 1 2 3 4 5 6 7 ... 12

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs908293	chr2:9942159-9942160	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	5 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs535256696	chr2:9942197-9942198	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
3	rs548807008	chr2:9942205-9942206	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
4	rs201223082	chr2:9942217-9942218	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
5	rs377068652	chr2:9942220-9942221	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
6	rs568933360	chr2:9942222-9942223	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
7	rs185054823	chr2:9942228-9942229	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
8	rs557846079	chr2:9942229-9942230	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
9	rs908294	chr2:9942269-9942270	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	5 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
10	rs533797568	chr2:9942298-9942299	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
11	rs144699819	chr2:9942328-9942329	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
12	rs573619262	chr2:9942345-9942346	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
13	rs542438178	chr2:9942362-9942363	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
14	rs187960586	chr2:9942364-9942365	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
15	rs575804429	chr2:9942376-9942377	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
16	rs544345374	chr2:9942387-9942388	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
17	rs564626054	chr2:9942572-9942573	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
18	rs533152836	chr2:9942585-9942586	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
19	rs558910136	chr2:9942596-9942597	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
20	rs34093163	chr2:9942605-9942606	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
21	rs537159823	chr2:9942652-9942653	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
22	rs560008179	chr2:9942671-9942672	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
23	rs367981256	chr2:9942735-9942736	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
24	rs529199606	chr2:9942768-9942769	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
25	rs548870399	chr2:9942796-9942797	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
26	rs568920409	chr2:9942797-9942798	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
27	rs192768369	chr2:9942808-9942809	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
28	rs183569747	chr2:9942839-9942840	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
29	rs201600275	chr2:9942848-9942849	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
30	rs386643046	chr2:9942890-9942891	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
31	rs116059159	chr2:9942891-9942892	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
32	rs553848464	chr2:9942923-9942924	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
33	rs567273651	chr2:9942952-9942953	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
34	rs536115149	chr2:9942959-9942960	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
35	rs13404061	chr2:9942990-9942991	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
36	rs34027844	chr2:9943011-9943012	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
37	rs575721272	chr2:9943035-9943036	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
38	rs576210887	chr2:9943052-9943053	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
39	rs557955856	chr2:9943076-9943077	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
40	rs577757956	chr2:9943083-9943084	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
41	rs116380420	chr2:9943118-9943119	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
42	rs386643047	chr2:9943127-9943128	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
43	rs115459169	chr2:9943128-9943129	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
44	rs542481843	chr2:9943152-9943153	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
45	rs562826235	chr2:9943185-9943186	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
46	rs531387402	chr2:9943197-9943198	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
47	rs551592033	chr2:9943198-9943199	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
48	rs147896304	chr2:9943212-9943213	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
49	rs541740333	chr2:9943230-9943231	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
50	rs76967621	chr2:9943256-9943257	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:60)

Disease	PMID	Source
Breast cancer	17133270	CNVD
Mental retardation	17847001	CNVD
Glioblastoma multiforme	21080181	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Cancer	20164920	CNVD
Neuroblastoma	21508638	CNVD
Breast cancer	17603634	CNVD
Cancer	16751803	CNVD
Neuroblastoma	16790693	CNVD
Colorectal cancer	16272173	CNVD
Breast cancer	17393978	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Medulloblastoma	21979893	CNVD
Lynch syndrome	18415027	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Ovarian neoplasms	16753589	CNVD
Glioblastoma multiforme	17387387	CNVD
Neuroblastoma	17533364	CNVD
Neuroblastoma	18923191	CNVD
Endometrial cancer	22040021	CNVD
Adrenal tumor	17535989	CNVD
Breast cancer	21264507	CNVD
Basal cell lymphoma	17053054	CNVD
Medulloblastoma	17522785	CNVD
Cancer	23418310	CNVD
Ewing''s sarcoma	21437220	CNVD
Ependymoma	16718352	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	18458336	CNVD
lymphocytic leukemia	21291569	CNVD
Prostate cancer	18632612	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Bladder cancer	21909424	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Cancer	20164919	CNVD
Hodgkin''s lymphoma	18641027	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Breast cancer	21364760	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Follicular lymphoma	20505157	CNVD
Autism	17483303	CNVD
Breast cancer	21804112	CNVD
Myelofibrosis	22110671	CNVD
Glioblastoma multiforme	22286061	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
Glioma	17123091	CNVD
Breast cancer	20409316	CNVD
Multiple myeloma	16616336	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Neuroblastoma	18923524	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:503 , 50 per page) page: 1 2 3 4 5 6 7 ... 11

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:9933200-9953800	Weak transcription	Fetal Heart	heart
2	chr2:9936600-9943800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:9937200-9943800	Enhancers	Esophagus	oesophagus
4	chr2:9937200-9944000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:9937200-9944200	Enhancers	Fetal Intestine Small	intestine
6	chr2:9937800-9943800	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr2:9938800-9942200	Enhancers	Fetal Thymus	thymus
8	chr2:9938800-9943600	Enhancers	Skeletal Muscle Male	skeletal muscle
9	chr2:9939000-9943200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr2:9939400-9943800	Enhancers	Fetal Muscle Leg	muscle
11	chr2:9939600-9942200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr2:9939600-9942200	Enhancers	Duodenum Smooth Muscle	Duodenum
13	chr2:9939600-9944000	Enhancers	Adipose Nuclei	Adipose
14	chr2:9939800-9942800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr2:9939800-9943800	Enhancers	NHDF-Ad	bronchial
16	chr2:9939800-9944200	Enhancers	Placenta	Placenta
17	chr2:9940000-9942200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr2:9940000-9942200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr2:9940000-9942200	Enhancers	Rectal Mucosa Donor 29	rectum
20	chr2:9940000-9943400	Enhancers	Placenta Amnion	Placenta Amnion
21	chr2:9940000-9944000	Enhancers	Fetal Intestine Large	intestine
22	chr2:9940000-9944000	Enhancers	NHLF	lung
23	chr2:9940200-9942200	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr2:9940200-9942200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr2:9940200-9942600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr2:9940200-9942800	Weak transcription	Pancreas	Pancrea
27	chr2:9940200-9944000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr2:9940400-9942600	Weak transcription	Colon Smooth Muscle	Colon
29	chr2:9940400-9942600	Enhancers	K562	blood
30	chr2:9940400-9943800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr2:9940400-9943800	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr2:9940400-9953600	Weak transcription	Right Atrium	heart
33	chr2:9940600-9942600	Weak transcription	Brain Cingulate Gyrus	brain
34	chr2:9940600-9949400	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr2:9940600-9949800	Weak transcription	Lung	lung
36	chr2:9940800-9942200	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr2:9940800-9942200	Flanking Bivalent TSS/Enh	HepG2	liver
38	chr2:9940800-9943800	Enhancers	HSMMtube	muscle
39	chr2:9940800-9944000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr2:9941000-9942200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr2:9941000-9942200	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr2:9941000-9942200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr2:9941000-9942200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
44	chr2:9941000-9942200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr2:9941000-9942200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr2:9941000-9942400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr2:9941000-9942400	Flanking Active TSS	Osteobl	bone
48	chr2:9941000-9943200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
49	chr2:9941000-9944000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr2:9941200-9942200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links