Variant report

Variant	nsv873898
Chromosome Location	chr2:40156882-40246716
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	chr2:40164512..40166990-chr2:40173493..40175018,2	MCF-7	breast:
2	chr2:40164512..40166990-chr2:40173493..40175018,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TMEM178-2	chr2:40185553-40185606	ucscGeneNc_uc002rrw_2

Extended variants
information (count: 5195 )
Associated
traits (count: 60 )

Variant overlapped rSNPs/rCNVs (count:5195 , 50 per page) page: 1 2 3 4 5 6 7 ... 104

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs13428022	chr2:40156882-40156883	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs563475748	chr2:40156899-40156900	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs565282899	chr2:40156900-40156901	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs369453580	chr2:40156904-40156905	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs530823586	chr2:40156930-40156931	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs549340170	chr2:40156952-40156953	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs192103900	chr2:40156975-40156976	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs528105106	chr2:40156983-40156984	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs145974997	chr2:40156985-40156986	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs199521060	chr2:40156991-40156992	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs571222877	chr2:40156997-40156998	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs538739208	chr2:40157032-40157033	Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs551553974	chr2:40157058-40157059	Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs377354991	chr2:40157105-40157106	Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs139879628	chr2:40157107-40157108	Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs184594417	chr2:40157143-40157144	Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs187822475	chr2:40157153-40157154	Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs543056225	chr2:40157165-40157166	Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs574296369	chr2:40157197-40157198	Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs374261312	chr2:40157205-40157206	Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs534674945	chr2:40157214-40157215	Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs6718981	chr2:40157217-40157218	Weak transcription Genic enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
23	rs144383403	chr2:40157219-40157220	Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs6544271	chr2:40157220-40157221	Weak transcription Genic enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
25	rs563464680	chr2:40157226-40157227	Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs146618023	chr2:40157228-40157229	Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs193288497	chr2:40157256-40157257	Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs561140332	chr2:40157274-40157275	Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs149216895	chr2:40157311-40157312	Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs546240181	chr2:40157313-40157314	Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs376091410	chr2:40157335-40157336	Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs564903212	chr2:40157350-40157351	Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs142458747	chr2:40157356-40157357	Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs184230537	chr2:40157379-40157380	Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs569891470	chr2:40157386-40157387	Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs537218776	chr2:40157412-40157413	Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs549179500	chr2:40157413-40157414	Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs11305417	chr2:40157473-40157474	Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs189644649	chr2:40157508-40157509	Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs151237416	chr2:40157554-40157555	Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs80179980	chr2:40157566-40157567	Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs578001703	chr2:40157579-40157580	Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs539121061	chr2:40157589-40157590	Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs557520224	chr2:40157613-40157614	Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs575832040	chr2:40157626-40157627	Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs565372787	chr2:40157631-40157632	Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs36048090	chr2:40157641-40157642	Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs542812542	chr2:40157774-40157775	Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs561148146	chr2:40157802-40157803	Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs573010272	chr2:40157812-40157813	Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:60)

Disease	PMID	Source
Breast cancer	17393978	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Breast cancer	17603634	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
Glioblastoma multiforme	21080181	CNVD
Ependymoma	16718352	CNVD
lymphocytic leukemia	21291569	CNVD
Prostate cancer	18632612	CNVD
Bladder cancer	21909424	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
Invasive pancreatic ductal carcinoma	16982739	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Esophageal adenocarcinoma	18519675	CNVD
Medulloblastoma	20607354	CNVD
Leukemia	18628472	CNVD
Autism	22495311	CNVD
Autism	19521722	CNVD
Autism	18522746	CNVD
Non-small cell lung cancer	18927303	CNVD
Breast cancer	21785460	CNVD
Lung cancer	18438408	CNVD
Prostate cancer	21965145	CNVD
Breast cancer	16397240	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Neuroblastoma	21508638	CNVD
Neurodevelopmental disorder	22521361	CNVD
Neurocytoma	17123091	CNVD
small cell lung cancer	20016488	CNVD
Melanoma	18172304	CNVD
Cancer	16751803	CNVD
Breast cancer	21364760	CNVD
Colorectal cancer	16272173	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD
Breast cancer	22522925	CNVD
Williams Syndrome	20824207	CNVD

Chromatin state (count:262 , 50 per page) page: 1 2 3 4 5 6

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40141600-40164800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr2:40147000-40167400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:40152000-40158800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr2:40155800-40157000	Strong transcription	Dnd41	blood
5	chr2:40156200-40157600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr2:40156400-40157600	Weak transcription	Fetal Thymus	thymus
7	chr2:40156400-40160200	Weak transcription	Fetal Stomach	stomach
8	chr2:40156800-40158600	Weak transcription	HSMM	muscle
9	chr2:40156800-40158800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr2:40157000-40159200	Genic enhancers	Dnd41	blood
11	chr2:40157600-40158000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr2:40157600-40158200	Enhancers	Thymus	Thymus
13	chr2:40157600-40158600	Enhancers	Fetal Thymus	thymus
14	chr2:40158600-40158800	Genic enhancers	Fetal Thymus	thymus
15	chr2:40158600-40159200	ZNF genes & repeats	HSMM	muscle
16	chr2:40158800-40159400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr2:40158800-40159400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr2:40158800-40159600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr2:40158800-40159600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr2:40158800-40164800	Weak transcription	Fetal Thymus	thymus
21	chr2:40159000-40159400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr2:40159000-40159600	Enhancers	NHEK	skin
23	chr2:40159200-40160200	Weak transcription	Dnd41	blood
24	chr2:40159200-40164800	Weak transcription	HSMM	muscle
25	chr2:40159400-40160000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr2:40159400-40165000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr2:40159600-40160000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr2:40159600-40162000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr2:40160000-40160600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr2:40160000-40161200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr2:40160200-40160400	Enhancers	Fetal Stomach	stomach
32	chr2:40160200-40164600	Enhancers	Dnd41	blood
33	chr2:40160400-40161000	Enhancers	Rectal Smooth Muscle	rectum
34	chr2:40160400-40161200	Weak transcription	Fetal Stomach	stomach
35	chr2:40160600-40164800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr2:40161200-40161400	Enhancers	Fetal Stomach	stomach
37	chr2:40161200-40165000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr2:40162000-40162600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr2:40164600-40166400	Flanking Active TSS	Dnd41	blood
40	chr2:40164800-40165000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr2:40164800-40166000	Enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr2:40164800-40166200	Enhancers	Fetal Thymus	thymus
43	chr2:40164800-40166400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr2:40164800-40166400	Enhancers	HSMM	muscle
45	chr2:40164800-40166400	Enhancers	Osteobl	bone
46	chr2:40165000-40165600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr2:40165000-40166400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr2:40165000-40166600	Enhancers	Muscle Satellite Cultured Cells	--
49	chr2:40165000-40166600	Enhancers	NH-A	brain
50	chr2:40165000-40166800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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