Variant report

Variant	esv1002221
Chromosome Location	chr20:16615972-16620221
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:16615631..16617548-chr20:16710088..16712046,2	MCF-7	breast:
2	chr20:16498174..16499663-chr20:16614502..16616040,11	MCF-7	breast:
3	chr20:16616652..16618800-chr20:16636562..16639329,2	MCF-7	breast:
4	chr20:16617985..16620145-chr20:16625485..16627795,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SNRPB2-1	chr20:16618897-16620313	XLOC_013467

Variant related genes	Relation type
ENSG00000125870	chromatin interactions
ENSG00000228809	chromatin interactions

Extended variants
information (count: 181 )
Associated
traits (count: 55 )

Variant overlapped rSNPs/rCNVs (count:181 , 50 per page) page: 1 2 3 4

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs188976653	chr20:16615982-16615983	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
2	rs117980168	chr20:16616001-16616002	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs545321744	chr20:16616017-16616018	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
4	rs13044376	chr20:16616033-16616034	Weak transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
5	rs372733154	chr20:16616057-16616058	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
6	rs549230626	chr20:16616086-16616087	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
7	rs535180873	chr20:16616092-16616093	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
8	rs34028245	chr20:16616109-16616110	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
9	rs74430914	chr20:16616110-16616111	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
10	rs181730631	chr20:16616172-16616173	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
11	rs528422335	chr20:16616174-16616175	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs546696984	chr20:16616185-16616186	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
13	rs537898865	chr20:16616200-16616201	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
14	rs571692712	chr20:16616220-16616221	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
15	rs187307606	chr20:16616257-16616258	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
16	rs6044185	chr20:16616336-16616337	Weak transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
17	rs577905306	chr20:16616337-16616338	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
18	rs569818386	chr20:16616376-16616377	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
19	rs369137733	chr20:16616380-16616381	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
20	rs372971030	chr20:16616384-16616385	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
21	rs537330560	chr20:16616405-16616406	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
22	rs190902361	chr20:16616421-16616422	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
23	rs145694800	chr20:16616506-16616507	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
24	rs556716581	chr20:16616574-16616575	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
25	rs557841169	chr20:16616578-16616579	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
26	rs577494671	chr20:16616603-16616604	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
27	rs534559345	chr20:16616612-16616613	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
28	rs552928470	chr20:16616678-16616679	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
29	rs577689698	chr20:16616693-16616694	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
30	rs545068548	chr20:16616701-16616702	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
31	rs369149780	chr20:16616706-16616707	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
32	rs73108768	chr20:16616735-16616736	Weak transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
33	rs575404931	chr20:16616738-16616739	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
34	rs367775191	chr20:16616773-16616774	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
35	rs542915637	chr20:16616815-16616816	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
36	rs4814520	chr20:16616817-16616818	Weak transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
37	rs528752170	chr20:16616856-16616857	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
38	rs73103324	chr20:16616882-16616883	Weak transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
39	rs565261128	chr20:16616950-16616951	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
40	rs532532560	chr20:16616974-16616975	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
41	rs117471244	chr20:16617044-16617045	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
42	rs569775293	chr20:16617083-16617084	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
43	rs537198106	chr20:16617086-16617087	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
44	rs549309492	chr20:16617092-16617093	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
45	rs146564980	chr20:16617093-16617094	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
46	rs541271804	chr20:16617108-16617109	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
47	rs13040341	chr20:16617199-16617200	Weak transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
48	rs533487636	chr20:16617210-16617211	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
49	rs182509792	chr20:16617230-16617231	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
50	rs552725327	chr20:16617254-16617255	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:55)

Disease	PMID	Source
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
Medulloblastoma	21979893	CNVD
Gastric cancer	17908304	CNVD
Urothelial carcinoma	21177765	CNVD
Acute myeloid leukemia	20729466	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Ewing''s sarcoma	17952124	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Thoracic aortic aneurysm	21092924	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
Ewing''s sarcoma	18628472	CNVD
Glioblastoma multiforme	18628472	CNVD
Leukemia	18628472	CNVD
Myelofibrosis	22110671	CNVD
Kabuki syndrome	21720541	CNVD
Glioblastoma multiforme	22286061	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Neurocytoma	17123091	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Breast cancer	21364760	CNVD
lymphocytic leukemia	21291569	CNVD

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:16605600-16628800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr20:16610400-16618400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr20:16615600-16618600	Weak transcription	Fetal Lung	lung
4	chr20:16615800-16620000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr20:16618400-16618600	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr20:16618400-16618600	Enhancers	Spleen	Spleen
7	chr20:16618400-16618800	Active TSS	Osteobl	bone
8	chr20:16618400-16620800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr20:16618600-16618800	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr20:16618600-16618800	Enhancers	Fetal Lung	lung
11	chr20:16618600-16619400	Enhancers	Fetal Stomach	stomach
12	chr20:16619200-16619400	Enhancers	Fetal Kidney	kidney
13	chr20:16619400-16619600	Bivalent Enhancer	Placenta	Placenta
14	chr20:16619400-16622400	Weak transcription	Fetal Kidney	kidney
15	chr20:16619600-16620000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr20:16619600-16620800	Enhancers	Fetal Intestine Small	intestine
17	chr20:16619800-16620600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr20:16619800-16620800	Enhancers	Fetal Intestine Large	intestine
19	chr20:16619800-16621600	Enhancers	Sigmoid Colon	Sigmoid Colon
20	chr20:16620000-16620400	Enhancers	HSMM	muscle
21	chr20:16620000-16620600	Enhancers	Rectal Mucosa Donor 29	rectum
22	chr20:16620000-16620800	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr20:16620000-16620800	Enhancers	Stomach Mucosa	stomach
24	chr20:16620200-16620800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links