Variant report

Variant	nsv585416
Chromosome Location	chr20:11156775-11190087
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:10640132..10642054-chr20:11188843..11191307,2	MCF-7	breast:
2	chr20:10654014..10656712-chr20:11187168..11189438,2	MCF-7	breast:
3	chr20:10655152..10655986-chr20:11185609..11186210,2	MCF-7	breast:
4	chr20:11185575..11186124-chr20:11254374..11255017,2	MCF-7	breast:
5	chr20:10676677..10677565-chr20:11185885..11186708,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-JAG1-10	chr20:11162818-11162937	NONHSAT078624

Variant related genes	Relation type
ENSG00000101384	chromatin interactions

Extended variants
information (count: 1432 )
Associated
traits (count: 62 )

Variant overlapped rSNPs/rCNVs (count:1432 , 50 per page) page: 1 2 3 4 5 6 7 ... 29

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs17225014	chr20:11156775-11156776	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs541633138	chr20:11156794-11156795	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs79842816	chr20:11156847-11156848	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs541504926	chr20:11156851-11156852	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs559957688	chr20:11156852-11156853	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs527482163	chr20:11156861-11156862	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs571723946	chr20:11156867-11156868	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs528775104	chr20:11156913-11156914	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs374061207	chr20:11156946-11156947	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs117107705	chr20:11156974-11156975	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs6134148	chr20:11157002-11157003	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs6040399	chr20:11157011-11157012	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance disease
13	rs371250702	chr20:11157018-11157019	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs544711492	chr20:11157027-11157028	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs6040400	chr20:11157036-11157037	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
16	rs556462505	chr20:11157038-11157039	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs183731575	chr20:11157116-11157117	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs550505024	chr20:11157149-11157150	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs544616415	chr20:11157192-11157193	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs564593656	chr20:11157210-11157211	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs79323078	chr20:11157244-11157245	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs8119166	chr20:11157266-11157267	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
23	rs187060733	chr20:11157346-11157347	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs117404765	chr20:11157401-11157402	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs190286230	chr20:11157429-11157430	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs550101357	chr20:11157432-11157433	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs8119301	chr20:11157440-11157441	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
28	rs182821172	chr20:11157441-11157442	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs186785831	chr20:11157445-11157446	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs375749261	chr20:11157461-11157462	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs571593658	chr20:11157477-11157478	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs376301761	chr20:11157483-11157484	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs191539934	chr20:11157502-11157503	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs371923191	chr20:11157509-11157510	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs374897849	chr20:11157514-11157515	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs373322327	chr20:11157518-11157519	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs386393304	chr20:11157519-11157520	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs539728253	chr20:11157522-11157523	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs185504970	chr20:11157523-11157524	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs536466921	chr20:11157526-11157527	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs386393305	chr20:11157536-11157537	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs71186129	chr20:11157537-11157538	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs142188859	chr20:11157551-11157552	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs538996954	chr20:11157602-11157603	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs151198334	chr20:11157621-11157622	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs141285427	chr20:11157639-11157640	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs146596850	chr20:11157664-11157665	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs189129924	chr20:11157669-11157670	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs574540524	chr20:11157696-11157697	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs13043918	chr20:11157730-11157731	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a

Variant related diseases (count:62)

Disease	PMID	Source
Medulloblastoma	21979893	CNVD
Breast cancer	16397240	CNVD
abortions and stillbirths	19751515	CNVD
Wilms tumour	21544195	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Breast cancer	16272173	CNVD
Melanoma	18172304	CNVD
Cancer	21637783	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Ewing''s sarcoma	21437220	CNVD
Oral cancer	19627613	CNVD
colon cancer	17210682	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	21080181	CNVD
Thyroid cancer	19087340	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Cancer	16751803	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Colorectal cancer	19359472	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Human rectal carcinomas	16397240	CNVD
Olfactory neuroblastoma	18408657	CNVD
Central neurocytomas	17123091	CNVD
Colorectal cancer	16272173	CNVD
Gastric cancer	17908304	CNVD
Urothelial carcinoma	21177765	CNVD
Acute myeloid leukemia	20729466	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Ewing''s sarcoma	17952124	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Lung cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Colorectal cancer	21645411	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Autism	22495311	CNVD
Glaucoma	21310917	CNVD
Alagille syndrome	22470819	CNVD
Lung cancer	16773561	CNVD
Renal cell carcinoma	18765545	CNVD
Alagille syndrome	17576883	CNVD
Anaplastic large cell lymphoma	18179710	CNVD
Prostate cancer	18632612	CNVD
Breast cancer	21804112	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Myelofibrosis	22110671	CNVD
Ewing''s sarcoma	18628472	CNVD
Glioblastoma multiforme	18628472	CNVD
Leukemia	18628472	CNVD
Breast cancer	20409316	CNVD
Cancer	20164919	CNVD
Non-syndromic sensorineural hearing loss	19587683	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:352 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:11149600-11158800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr20:11151600-11159400	Weak transcription	A549	lung
3	chr20:11151800-11158600	Weak transcription	HUVEC	blood vessel
4	chr20:11152800-11159400	Weak transcription	HSMM	muscle
5	chr20:11155400-11158600	Weak transcription	NH-A	brain
6	chr20:11156600-11157200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr20:11157200-11159400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr20:11158200-11160600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr20:11158400-11160200	Enhancers	Muscle Satellite Cultured Cells	--
10	chr20:11158400-11160400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr20:11158400-11160400	Enhancers	NHEK	skin
12	chr20:11158600-11160600	Enhancers	NH-A	brain
13	chr20:11158600-11161000	Enhancers	HUVEC	blood vessel
14	chr20:11158800-11159200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr20:11159000-11160600	Enhancers	HMEC	breast
16	chr20:11159200-11160400	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr20:11159200-11161200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr20:11159400-11159800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr20:11159400-11159800	Enhancers	Fetal Heart	heart
20	chr20:11159400-11159800	Enhancers	HSMM	muscle
21	chr20:11159400-11160000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr20:11159400-11160200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr20:11159400-11160200	Enhancers	A549	lung
24	chr20:11159600-11160000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr20:11159600-11160000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr20:11159600-11160000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr20:11159600-11160000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr20:11159600-11160000	Enhancers	Hela-S3	cervix
29	chr20:11159600-11160000	Enhancers	HSMMtube	muscle
30	chr20:11159600-11160000	Enhancers	NHLF	lung
31	chr20:11159600-11160000	Enhancers	Osteobl	bone
32	chr20:11159600-11160200	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr20:11159600-11160600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr20:11159600-11163200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr20:11160000-11168000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr20:11160400-11160600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr20:11160400-11160800	Weak transcription	NHEK	skin
38	chr20:11160600-11160800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr20:11160600-11161200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr20:11160800-11161000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr20:11160800-11162200	ZNF genes & repeats	NHEK	skin
42	chr20:11161000-11162200	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr20:11161200-11162800	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr20:11161200-11163600	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr20:11162200-11165000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr20:11162800-11165000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr20:11163000-11163200	Enhancers	Monocytes-CD14+_RO01746	blood
48	chr20:11163000-11164200	Enhancers	Primary monocytes fromperipheralblood	blood
49	chr20:11163000-11164400	Enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr20:11163200-11163400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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