Variant report

Variant	nsv1006550
Chromosome Location	chr2:40164769-40209936
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: 2551 )
Associated
traits (count: 60 )

Variant overlapped rSNPs/rCNVs (count:2551 , 50 per page) page: 1 2 3 4 5 6 7 ... 52

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs145773952	chr2:40164769-40164770	Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
2	rs558036607	chr2:40164808-40164809	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
3	rs185067390	chr2:40164826-40164827	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
4	rs73924712	chr2:40164833-40164834	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
5	rs188316370	chr2:40164851-40164852	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
6	rs575080582	chr2:40164871-40164872	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
7	rs181062752	chr2:40164889-40164890	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
8	rs148963011	chr2:40164916-40164917	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
9	rs376543101	chr2:40164928-40164929	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
10	rs1861259	chr2:40165002-40165003	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
11	rs557671176	chr2:40165020-40165021	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
12	rs575887872	chr2:40165055-40165056	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
13	rs545920184	chr2:40165060-40165061	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
14	rs563922174	chr2:40165103-40165104	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
15	rs534449967	chr2:40165133-40165134	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
16	rs556092330	chr2:40165142-40165143	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
17	rs113590051	chr2:40165165-40165166	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
18	rs549969308	chr2:40165189-40165190	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
19	rs561785122	chr2:40165202-40165203	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
20	rs529194159	chr2:40165230-40165231	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
21	rs186579254	chr2:40165234-40165235	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
22	rs565724383	chr2:40165253-40165254	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
23	rs539527057	chr2:40165254-40165255	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
24	rs551469070	chr2:40165278-40165279	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
25	rs191476813	chr2:40165318-40165319	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
26	rs79774409	chr2:40165361-40165362	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
27	rs150995649	chr2:40165373-40165374	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
28	rs575024584	chr2:40165390-40165391	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
29	rs536192302	chr2:40165392-40165393	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
30	rs4670299	chr2:40165395-40165396	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
31	rs572140557	chr2:40165396-40165397	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
32	rs78804931	chr2:40165397-40165398	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
33	rs369301842	chr2:40165417-40165418	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
34	rs564213054	chr2:40165421-40165422	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
35	rs183743223	chr2:40165429-40165430	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
36	rs186873489	chr2:40165443-40165444	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
37	rs561956962	chr2:40165479-40165480	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
38	rs529169220	chr2:40165565-40165566	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
39	rs547750117	chr2:40165595-40165596	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
40	rs545197167	chr2:40165598-40165599	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
41	rs559701374	chr2:40165613-40165614	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
42	rs191017263	chr2:40165614-40165615	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
43	rs551402207	chr2:40165621-40165622	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
44	rs141063265	chr2:40165641-40165642	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
45	rs58096789	chr2:40165715-40165716	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
46	rs377465262	chr2:40165718-40165719	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
47	rs183531140	chr2:40165733-40165734	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
48	rs115870783	chr2:40165802-40165803	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
49	rs186627239	chr2:40165813-40165814	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
50	rs554008444	chr2:40165848-40165849	Enhancers Weak transcription Flanking Active TSS	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:134 , 50 per page) page: 1 2 3

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	chr2:40158800-40164800	Weak transcription	Fetal Thymus	thymus
4	chr2:40159200-40164800	Weak transcription	HSMM	muscle
5	chr2:40159400-40165000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr2:40160600-40164800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr2:40161200-40165000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr2:40164600-40166400	Flanking Active TSS	Dnd41	blood
9	chr2:40164800-40165000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr2:40164800-40166000	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr2:40164800-40166200	Enhancers	Fetal Thymus	thymus
12	chr2:40164800-40166400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr2:40164800-40166400	Enhancers	HSMM	muscle
14	chr2:40164800-40166400	Enhancers	Osteobl	bone
15	chr2:40165000-40165600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr2:40165000-40166400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr2:40165000-40166600	Enhancers	Muscle Satellite Cultured Cells	--
18	chr2:40165000-40166600	Enhancers	NH-A	brain
19	chr2:40165000-40166800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr2:40165000-40175800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr2:40165200-40165600	Enhancers	HSMMtube	muscle
22	chr2:40165200-40166000	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr2:40165200-40166400	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr2:40165200-40166400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr2:40165400-40165800	Enhancers	Thymus	Thymus
26	chr2:40165400-40166400	Enhancers	HMEC	breast
27	chr2:40165600-40169400	Weak transcription	HSMMtube	muscle
28	chr2:40165600-40175200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr2:40166400-40168200	Enhancers	Dnd41	blood
30	chr2:40166400-40169400	Weak transcription	HSMM	muscle
31	chr2:40166400-40169800	Weak transcription	Osteobl	bone
32	chr2:40166600-40169600	Weak transcription	NH-A	brain
33	chr2:40166600-40170000	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr2:40166800-40167200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr2:40166800-40168400	Weak transcription	Fetal Thymus	thymus
36	chr2:40167200-40167400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr2:40167400-40167600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr2:40167400-40170200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr2:40167600-40167800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr2:40169400-40170600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr2:40169400-40170600	Enhancers	Dnd41	blood
42	chr2:40169400-40170600	Enhancers	HSMM	muscle
43	chr2:40169400-40170600	Enhancers	HSMMtube	muscle
44	chr2:40169400-40170800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr2:40169600-40170000	Enhancers	NH-A	brain
46	chr2:40169800-40170600	Enhancers	Osteobl	bone
47	chr2:40170000-40170600	Enhancers	Muscle Satellite Cultured Cells	--
48	chr2:40170000-40174600	Weak transcription	NH-A	brain
49	chr2:40170200-40170600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr2:40170200-40170600	Enhancers	NHDF-Ad	bronchial

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