Variant report

Variant	esv3344936
Chromosome Location	chr2:10339031-10342870
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:10331138..10333960-chr2:10340461..10341964,2	K562	blood:
2	chr2:10339278..10341450-chr2:10342848..10344717,2	K562	blood:
3	chr2:10339278..10341450-chr2:10342848..10344717,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CYS1-7	chr2:10341367-10341629	NONHSAT069093
2	lnc-CYS1-7	chr2:10338881-10339400	NONHSAT069093

Variant related genes	Relation type
ENSG00000265418	chromatin interactions

Extended variants
information (count: 207 )
Associated
traits (count: 59 )

Variant overlapped rSNPs/rCNVs (count:207 , 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	rs540659543	chr2:10339048-10339049	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
2	rs112687657	chr2:10339079-10339080	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
3	rs577282594	chr2:10339082-10339083	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
4	rs139674675	chr2:10339084-10339085	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
5	rs567590613	chr2:10339100-10339101	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
6	rs1035122	chr2:10339147-10339148	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs530275135	chr2:10339177-10339178	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
8	rs189511239	chr2:10339186-10339187	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
9	rs144434303	chr2:10339194-10339195	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
10	rs150670496	chr2:10339201-10339202	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
11	rs543645062	chr2:10339220-10339221	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
12	rs375312897	chr2:10339221-10339222	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
13	rs546596013	chr2:10339236-10339237	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
14	rs571215299	chr2:10339283-10339284	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
15	rs538730919	chr2:10339327-10339328	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
16	rs139956683	chr2:10339328-10339329	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
17	rs550451034	chr2:10339332-10339333	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
18	rs138545035	chr2:10339404-10339405	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs386389514	chr2:10339405-10339406	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs113107712	chr2:10339411-10339412	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs113607633	chr2:10339414-10339415	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs75705654	chr2:10339415-10339416	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs61224448	chr2:10339416-10339417	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs113040795	chr2:10339420-10339421	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs4583436	chr2:10339433-10339434	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
26	rs536488513	chr2:10339472-10339473	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs554884624	chr2:10339478-10339479	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs149852213	chr2:10339503-10339504	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs546749603	chr2:10339532-10339533	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs75440124	chr2:10339533-10339534	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs533908534	chr2:10339535-10339536	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs558918849	chr2:10339538-10339539	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs201708643	chr2:10339633-10339634	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs181848039	chr2:10339634-10339635	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs200254209	chr2:10339635-10339636	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs574676585	chr2:10339641-10339642	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs542045326	chr2:10339678-10339679	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs377409012	chr2:10339682-10339683	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs527989993	chr2:10339683-10339684	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs533216777	chr2:10339690-10339691	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs543738465	chr2:10339701-10339702	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs546233764	chr2:10339703-10339704	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs56051374	chr2:10339704-10339705	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
44	rs532052008	chr2:10339712-10339713	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs372229239	chr2:10339724-10339725	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs13024482	chr2:10339766-10339767	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs77232389	chr2:10339767-10339768	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs548422103	chr2:10339778-10339779	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs566730248	chr2:10339784-10339785	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs186704055	chr2:10339798-10339799	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:59)

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
Esophageal adenocarcinoma	18519675	CNVD
Ependymoma	18628472	CNVD
Leukemia	18628472	CNVD

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:10290200-10351400	Strong transcription	Dnd41	blood
2	chr2:10304400-10339800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr2:10313000-10344400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr2:10314000-10340400	Weak transcription	HepG2	liver
5	chr2:10325600-10342800	Weak transcription	Fetal Brain Female	brain
6	chr2:10326600-10339400	Strong transcription	Thymus	Thymus
7	chr2:10333000-10347000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr2:10335200-10348600	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr2:10336800-10344600	Weak transcription	Brain Hippocampus Middle	brain
10	chr2:10337200-10342800	Weak transcription	Gastric	stomach
11	chr2:10337200-10349600	Weak transcription	Spleen	Spleen
12	chr2:10337600-10342800	Weak transcription	Fetal Brain Male	brain
13	chr2:10337800-10339400	ZNF genes & repeats	Fetal Stomach	stomach
14	chr2:10338000-10339400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
15	chr2:10338000-10339400	ZNF genes & repeats	Fetal Intestine Small	intestine
16	chr2:10338200-10339200	Strong transcription	Fetal Thymus	thymus
17	chr2:10338600-10339200	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr2:10338600-10351200	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr2:10338800-10339400	Strong transcription	Fetal Muscle Leg	muscle
20	chr2:10338800-10342400	Weak transcription	K562	blood
21	chr2:10338800-10344400	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr2:10339200-10345400	Weak transcription	Fetal Thymus	thymus
23	chr2:10339200-10345600	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr2:10339400-10342400	Weak transcription	Fetal Stomach	stomach
25	chr2:10339400-10342600	Weak transcription	Fetal Muscle Leg	muscle
26	chr2:10339400-10343000	Weak transcription	Thymus	Thymus
27	chr2:10339400-10350600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr2:10339400-10362000	Weak transcription	Fetal Intestine Small	intestine
29	chr2:10340000-10344000	Weak transcription	Brain Germinal Matrix	brain
30	chr2:10340400-10341800	Enhancers	HepG2	liver
31	chr2:10340400-10344400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr2:10341000-10341800	Enhancers	Fetal Intestine Large	intestine
33	chr2:10341800-10342400	Weak transcription	Fetal Intestine Large	intestine
34	chr2:10341800-10354400	Weak transcription	HepG2	liver
35	chr2:10342200-10342800	Bivalent Enhancer	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr2:10342200-10348600	Weak transcription	A549	lung
37	chr2:10342400-10342600	Enhancers	Fetal Intestine Large	intestine
38	chr2:10342400-10342800	Enhancers	K562	blood
39	chr2:10342400-10343000	Enhancers	HMEC	breast
40	chr2:10342400-10343600	Enhancers	Fetal Stomach	stomach
41	chr2:10342600-10343000	Enhancers	Left Ventricle	heart
42	chr2:10342600-10343200	Enhancers	Fetal Lung	lung
43	chr2:10342600-10343400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr2:10342600-10343600	Enhancers	Muscle Satellite Cultured Cells	--
45	chr2:10342600-10343600	Enhancers	HSMMtube	muscle
46	chr2:10342600-10344200	Enhancers	Fetal Muscle Leg	muscle
47	chr2:10342800-10343000	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr2:10342800-10343000	Enhancers	Gastric	stomach
49	chr2:10342800-10343600	Enhancers	Right Ventricle	heart
50	chr2:10342800-10343600	Enhancers	HSMM	muscle

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