Variant report

Variant	nsv1005729
Chromosome Location	chr2:56750209-56778009
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	chr2:56773723..56776584-chr8:126325913..126327457,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CCDC85A-1	chr2:56750279-56750484	NONHSAT070827
2	lnc-CCDC85A-1	chr2:56750280-56750484	XLOC_001482

Variant related genes	Relation type
NR2E1	miRNA target sites

Extended variants
information (count: 816 )
Associated
traits (count: 82 )

Variant overlapped rSNPs/rCNVs (count:816 , 50 per page) page: 1 2 3 4 5 6 7 ... 17

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs17268931	chr2:56750209-56750210	Flanking Active TSS Enhancers Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs543176700	chr2:56750211-56750212	Flanking Active TSS Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
3	rs140959903	chr2:56750246-56750247	Flanking Active TSS Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
4	rs180976216	chr2:56750302-56750303	Flanking Active TSS Enhancers Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
5	rs184814868	chr2:56750337-56750338	Flanking Active TSS Enhancers Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
6	rs189635103	chr2:56750343-56750344	Flanking Active TSS Enhancers Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
7	rs113284281	chr2:56750397-56750398	Flanking Active TSS Enhancers Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
8	rs17048063	chr2:56750425-56750426	Flanking Active TSS Enhancers Weak transcription Active TSS	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
9	rs547482189	chr2:56750429-56750430	Flanking Active TSS Enhancers Weak transcription Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
10	rs567722086	chr2:56750444-56750445	Flanking Active TSS Enhancers Weak transcription Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
11	rs536329158	chr2:56750446-56750447	Flanking Active TSS Enhancers Weak transcription Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
12	rs569732136	chr2:56750506-56750507	Flanking Active TSS Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
13	rs150192845	chr2:56750517-56750518	Flanking Active TSS Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
14	rs569508401	chr2:56750522-56750523	Flanking Active TSS Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
15	rs138961773	chr2:56750537-56750538	Flanking Active TSS Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
16	rs370419326	chr2:56750563-56750564	Flanking Active TSS Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
17	rs181705828	chr2:56750569-56750570	Flanking Active TSS Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
18	rs199670477	chr2:56750594-56750595	Flanking Active TSS Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
19	rs35971356	chr2:56750676-56750677	Flanking Active TSS Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
20	rs186117967	chr2:56750683-56750684	Flanking Active TSS Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
21	rs190879926	chr2:56750730-56750731	Flanking Active TSS Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
22	rs17048064	chr2:56750753-56750754	Flanking Active TSS Enhancers Weak transcription Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
23	rs574401245	chr2:56750756-56750757	Flanking Active TSS Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
24	rs543136150	chr2:56750766-56750767	Flanking Active TSS Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
25	rs17048067	chr2:56750788-56750789	Flanking Active TSS Enhancers Weak transcription Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
26	rs140708694	chr2:56750793-56750794	Flanking Active TSS Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
27	rs145864957	chr2:56750829-56750830	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
28	rs73940707	chr2:56750868-56750869	Enhancers Weak transcription Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
29	rs368848929	chr2:56750920-56750921	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
30	rs78030502	chr2:56750924-56750925	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
31	rs181905029	chr2:56750927-56750928	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
32	rs548100028	chr2:56750977-56750978	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
33	rs17048070	chr2:56750992-56750993	Enhancers Weak transcription Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
34	rs574933584	chr2:56751019-56751020	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs530150925	chr2:56751028-56751029	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs549862197	chr2:56751040-56751041	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs569818225	chr2:56751052-56751053	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs536646465	chr2:56751066-56751067	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs374169487	chr2:56751107-56751108	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs538408447	chr2:56751135-56751136	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs186592126	chr2:56751148-56751149	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs1030332	chr2:56751173-56751174	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
43	rs534590261	chr2:56751180-56751181	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs554879753	chr2:56751182-56751183	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs4672123	chr2:56751213-56751214	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
46	rs1030331	chr2:56751231-56751232	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
47	rs75146827	chr2:56751239-56751240	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs551709243	chr2:56751240-56751241	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs545582950	chr2:56751287-56751288	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs565457905	chr2:56751306-56751307	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:82)

Disease	PMID	Source
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
Breast cancer	17603634	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Ependymoma	16718352	CNVD
lymphocytic leukemia	21291569	CNVD
Prostate cancer	18632612	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Intellectual disability	22102821	CNVD
Cancer	20164919	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Follicular lymphoma	20505157	CNVD
Autism	17483303	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Esophageal adenocarcinoma	18519675	CNVD
Medulloblastoma	20607354	CNVD
Leukemia	18628472	CNVD
Autism	22495311	CNVD
Autism	18522746	CNVD
Breast cancer	21785460	CNVD
Lung cancer	18438408	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Neuroblastoma	21508638	CNVD
Neurodevelopmental disorder	22521361	CNVD
Melanoma	18172304	CNVD
Cancer	16751803	CNVD
Colorectal cancer	16272173	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Williams Syndrome	20824207	CNVD
Breast cancer	16272173	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Ovarian cancer	21720365	CNVD
abnormal development	18461090	CNVD
Retinoblastoma	22278416	CNVD
Cancer	21183584	CNVD
Breast cancer	16397240	CNVD
Chronic lymphocytic leukemia	17053054	CNVD
Hereditary non-polyposis colorectal cancer	19566914	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
small cell lung cancer	20016488	CNVD
Developmental delay	21147756	CNVD
Mental retardation	19951919	CNVD
Myelofibrosis	22110671	CNVD
Microcephaly	20799320	CNVD
camptodactyly	20799320	CNVD
cognitive delay	20799320	CNVD
prenatal and postnatal growth deficiency	20799320	CNVD
ptosis of eyelids	20799320	CNVD
Maculopathy	20981449	CNVD
2p16.1 microdeletion syndrome	22283845	CNVD
Autism	22579565	CNVD
Autism	16963482	CNVD
Autism	21750575	CNVD
idiopathic intellectual disability	16963482	CNVD
Carcinoma ex pleomorphic adenoma	18828159	CNVD
Multiple myeloma	16616336	CNVD
Follicular lymphoma	17699855	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Pancreatic ductal adenocarcinoma	19077451	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Seminomas	18059402	CNVD
Testicular germ cell tumor	18059402	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:56748800-56752600	Enhancers	Fetal Heart	heart
2	chr2:56749600-56750600	Enhancers	Liver	Liver
3	chr2:56749600-56751800	Enhancers	HSMM	muscle
4	chr2:56749800-56750400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr2:56749800-56750400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr2:56749800-56750400	Enhancers	Colon Smooth Muscle	Colon
7	chr2:56749800-56750400	Enhancers	Duodenum Mucosa	Duodenum
8	chr2:56749800-56750400	Enhancers	Hela-S3	cervix
9	chr2:56749800-56750600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr2:56749800-56750600	Enhancers	Fetal Stomach	stomach
11	chr2:56749800-56750600	Enhancers	Psoas Muscle	Psoas
12	chr2:56749800-56750600	Enhancers	HSMMtube	muscle
13	chr2:56749800-56751400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr2:56749800-56751400	Enhancers	Muscle Satellite Cultured Cells	--
15	chr2:56750000-56750400	Enhancers	Skeletal Muscle Female	skeletal muscle
16	chr2:56750000-56750400	Flanking Active TSS	A549	lung
17	chr2:56750000-56750600	Enhancers	NHEK	skin
18	chr2:56750200-56750400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
19	chr2:56750200-56750600	Enhancers	Adipose Nuclei	Adipose
20	chr2:56750200-56750800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr2:56750200-56751000	Active TSS	Fetal Muscle Leg	muscle
22	chr2:56750400-56750600	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr2:56750400-56750600	Active TSS	Skeletal Muscle Female	skeletal muscle
24	chr2:56750400-56750600	Enhancers	A549	lung
25	chr2:56750400-56751400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr2:56750600-56758200	Weak transcription	Psoas Muscle	Psoas
27	chr2:56750800-56752000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr2:56751600-56751800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr2:56758200-56758800	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr2:56758200-56759200	Enhancers	Psoas Muscle	Psoas
31	chr2:56758800-56759400	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr2:56758800-56759800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr2:56758800-56759800	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr2:56758800-56760000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr2:56758800-56762400	Enhancers	Muscle Satellite Cultured Cells	--
36	chr2:56759000-56762200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr2:56759400-56759600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr2:56759600-56761000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr2:56759800-56760000	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr2:56759800-56761200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr2:56760000-56761000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr2:56760400-56760600	Enhancers	HUES6 Cell Line	embryonic stem cell
43	chr2:56760400-56762400	Enhancers	HSMM	muscle
44	chr2:56761000-56762000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr2:56761000-56762200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr2:56761200-56761400	Enhancers	HUES6 Cell Line	embryonic stem cell
47	chr2:56761200-56761400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr2:56761200-56762000	Enhancers	HSMMtube	muscle
49	chr2:56761400-56761800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr2:56761800-56762200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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