Variant report

Variant	esv3361205
Chromosome Location	chr20:25046552-25049950
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:25046117..25046996-chr20:25159492..25160465,5	MCF-7	breast:
2	chr20:24980910..24981445-chr20:25046435..25046961,2	MCF-7	breast:
3	chr20:25043693..25045702-chr20:25047001..25049231,2	MCF-7	breast:
4	chr20:24975151..24976233-chr20:25045881..25047015,16	MCF-7	breast:
5	chr20:24972253..24980445-chr20:25044479..25049663,13	MCF-7	breast:
6	chr20:25046140..25046670-chr20:25159575..25160213,2	MCF-7	breast:
7	chr20:24974024..24975149-chr20:25046038..25047090,7	MCF-7	breast:
8	chr20:25048502..25051261-chr20:25062095..25064063,2	MCF-7	breast:
9	chr20:24975304..24980368-chr20:25042845..25047055,6	MCF-7	breast:
10	chr20:24980657..24981409-chr20:25046140..25046996,4	MCF-7	breast:
11	chr20:24974184..24976552-chr20:25044724..25047326,32	MCF-7	breast:
12	chr20:24974985..24976149-chr20:25046073..25047055,8	K562	blood:
13	chr20:25046045..25046980-chr20:25057133..25058078,4	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ACSS1-1	chr20:25047157-25047179	NONHSAT079124

No data

Variant related genes	Relation type
ENSG00000101474	chromatin interactions
ENSG00000100987	chromatin interactions

Extended variants
information (count: 173 )
Associated
traits (count: 55 )

Variant overlapped rSNPs/rCNVs (count:173 , 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	rs59758051	chr20:25046610-25046611	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs181140615	chr20:25046680-25046681	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs185151965	chr20:25046693-25046694	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
4	rs547536647	chr20:25046697-25046698	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs564524255	chr20:25046750-25046751	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
6	rs188000881	chr20:25046759-25046760	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs533315960	chr20:25046769-25046770	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs528414778	chr20:25046820-25046821	Weak transcription Enhancers Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs550502881	chr20:25046830-25046831	Weak transcription Enhancers Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs570410497	chr20:25046840-25046841	Weak transcription Enhancers Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs558564435	chr20:25046858-25046859	Weak transcription Enhancers Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs199817815	chr20:25046893-25046894	Weak transcription Enhancers Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs147043273	chr20:25046895-25046896	Weak transcription Enhancers Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs199651487	chr20:25046896-25046897	Weak transcription Enhancers Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs386393576	chr20:25046903-25046904	Weak transcription Enhancers Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs139793942	chr20:25046915-25046916	Weak transcription Enhancers Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs72160036	chr20:25046928-25046929	Weak transcription Enhancers Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs61688808	chr20:25046931-25046932	Weak transcription Enhancers Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs11474476	chr20:25046938-25046939	Weak transcription Enhancers Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs6050292	chr20:25046949-25046950	Weak transcription Enhancers Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs376175944	chr20:25047174-25047175	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
22	rs370528712	chr20:25047190-25047191	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs566106343	chr20:25047201-25047202	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
24	rs79240119	chr20:25047215-25047216	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
25	rs368111868	chr20:25047258-25047259	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs577229632	chr20:25047270-25047271	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs536687920	chr20:25047398-25047399	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
28	rs553123556	chr20:25047409-25047410	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs556534391	chr20:25047449-25047450	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
30	rs577112570	chr20:25047518-25047519	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
31	rs541407651	chr20:25047634-25047635	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs573626055	chr20:25047638-25047639	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
33	rs182019230	chr20:25047677-25047678	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs199884232	chr20:25047738-25047739	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs112615721	chr20:25047740-25047741	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs202188289	chr20:25047756-25047757	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs201759754	chr20:25047764-25047765	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
38	rs145014967	chr20:25047765-25047766	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
39	rs140540338	chr20:25047766-25047767	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
40	rs6115020	chr20:25047779-25047780	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs201023054	chr20:25047785-25047786	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
42	rs372504657	chr20:25047790-25047791	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
43	rs373078753	chr20:25047796-25047797	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
44	rs377531977	chr20:25047797-25047798	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
45	rs369777358	chr20:25047799-25047800	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
46	rs376328625	chr20:25047802-25047803	ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs61084774	chr20:25047809-25047810	ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
48	rs373232567	chr20:25047817-25047818	ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
49	rs6050293	chr20:25047830-25047831	ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
50	rs370362543	chr20:25047836-25047837	ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:55)

Disease	PMID	Source
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
Renal cell carcinoma	18765545	CNVD
Alagille syndrome	17576883	CNVD
Anaplastic large cell lymphoma	18179710	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Cancer	21183584	CNVD
Myxofibrosarcoma	16751306	CNVD
Pancreatic endocrine tumor	17639061	CNVD
Breast cancer	16608533	CNVD
Bladder cancer	21909424	CNVD
Esophageal cancer	21851588	CNVD
Breast cancer	17133270	CNVD
Thrombophilia	17576883	CNVD
Myelofibrosis	22110671	CNVD
Mental retardation	21062444	CNVD
Hepatocellular carcinoma	22174799	CNVD
Barrett''s adenocarcinoma	18663352	CNVD
Chordoma	18071362	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	21364760	CNVD
Oral cancer	21386901	CNVD

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25044600-25047800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr20:25044800-25046800	Enhancers	Brain Anterior Caudate	brain
3	chr20:25044800-25046800	Enhancers	Brain Inferior Temporal Lobe	brain
4	chr20:25044800-25047400	Enhancers	Placenta	Placenta
5	chr20:25045000-25047400	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr20:25045200-25046600	Enhancers	Brain Cingulate Gyrus	brain
7	chr20:25045200-25046800	Enhancers	Brain Hippocampus Middle	brain
8	chr20:25045200-25046800	Enhancers	Stomach Mucosa	stomach
9	chr20:25045200-25047200	Enhancers	Fetal Intestine Large	intestine
10	chr20:25045400-25046800	Enhancers	Fetal Intestine Small	intestine
11	chr20:25045400-25047800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr20:25045600-25046600	Flanking Active TSS	HepG2	liver
13	chr20:25045600-25046800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr20:25045600-25046800	Enhancers	Liver	Liver
15	chr20:25045800-25046600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr20:25045800-25046600	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr20:25045800-25046600	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
18	chr20:25045800-25046800	Enhancers	Primary B cells from peripheral blood	blood
19	chr20:25045800-25046800	Flanking Active TSS	Duodenum Mucosa	Duodenum
20	chr20:25045800-25046800	Enhancers	Rectal Mucosa Donor 29	rectum
21	chr20:25045800-25048000	Enhancers	Gastric	stomach
22	chr20:25046000-25046600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
23	chr20:25046000-25046800	Enhancers	Right Atrium	heart
24	chr20:25046200-25046600	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
25	chr20:25046200-25046600	Enhancers	Primary B cells from cord blood	blood
26	chr20:25046200-25046600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr20:25046200-25046600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
28	chr20:25046200-25046600	Enhancers	Colon Smooth Muscle	Colon
29	chr20:25046200-25046600	Enhancers	Duodenum Smooth Muscle	Duodenum
30	chr20:25046200-25046800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
31	chr20:25046200-25046800	Enhancers	Primary T killer memory cells from peripheral blood	blood
32	chr20:25046200-25046800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
33	chr20:25046200-25046800	Enhancers	Fetal Heart	heart
34	chr20:25046200-25046800	Enhancers	Placenta Amnion	Placenta Amnion
35	chr20:25046200-25047000	Enhancers	Primary T helper cells PMA-I stimulated	--
36	chr20:25046200-25047400	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr20:25046200-25047800	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr20:25046400-25046600	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr20:25046400-25046600	Bivalent Enhancer	Fetal Stomach	stomach
40	chr20:25046400-25047200	Weak transcription	Pancreas	Pancrea
41	chr20:25046400-25047800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr20:25046400-25047800	Weak transcription	Lung	lung
43	chr20:25046400-25047800	Weak transcription	Right Ventricle	heart
44	chr20:25046400-25048000	Weak transcription	Esophagus	oesophagus
45	chr20:25046400-25048000	Weak transcription	Spleen	Spleen
46	chr20:25046400-25057200	Weak transcription	Brain Substantia Nigra	brain
47	chr20:25046600-25046800	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
48	chr20:25046600-25046800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
49	chr20:25046600-25046800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
50	chr20:25046600-25046800	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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