Variant report

Variant	esv3359123
Chromosome Location	chr20:25449069-25450002
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	chr17:59433764..59435297-chr20:25448424..25451207,2	MCF-7	breast:

Extended variants
information (count: 67 )
Associated
traits (count: 56 )

Variant overlapped rSNPs/rCNVs (count:67 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs184114196	chr20:25449106-25449107	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs375675347	chr20:25449127-25449128	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs545282405	chr20:25449164-25449165	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs142756060	chr20:25449170-25449171	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs56352955	chr20:25449172-25449173	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs378240	chr20:25449174-25449175	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	mRNA abundance
7	rs575826391	chr20:25449179-25449180	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs188464546	chr20:25449195-25449196	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs368273502	chr20:25449307-25449308	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs560910720	chr20:25449335-25449336	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs530057053	chr20:25449389-25449390	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs181021120	chr20:25449392-25449393	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs58238985	chr20:25449417-25449418	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs527452852	chr20:25449431-25449432	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs61638282	chr20:25449444-25449445	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs560389287	chr20:25449451-25449452	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs552502391	chr20:25449456-25449457	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs532682324	chr20:25449461-25449462	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs199511867	chr20:25449463-25449464	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs372939946	chr20:25449473-25449474	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs552087210	chr20:25449513-25449514	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs368782	chr20:25449530-25449531	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs569064165	chr20:25449533-25449534	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs368770	chr20:25449539-25449540	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs112066719	chr20:25449560-25449561	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs368736	chr20:25449567-25449568	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs368724	chr20:25449576-25449577	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs150612294	chr20:25449595-25449596	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs535185226	chr20:25449647-25449648	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs184430199	chr20:25449656-25449657	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs112555823	chr20:25449674-25449675	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs533774033	chr20:25449687-25449688	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs553932196	chr20:25449688-25449689	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs371476994	chr20:25449700-25449701	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs570449418	chr20:25449703-25449704	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs375727436	chr20:25449704-25449705	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs558867003	chr20:25449733-25449734	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs531622383	chr20:25449761-25449762	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs575810406	chr20:25449779-25449780	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs544473485	chr20:25449780-25449781	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs71332657	chr20:25449797-25449798	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs13045622	chr20:25449798-25449799	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs13044451	chr20:25449799-25449800	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs13044443	chr20:25449814-25449815	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs78974022	chr20:25449817-25449818	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs367666	chr20:25449818-25449819	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
47	rs74790484	chr20:25449833-25449834	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs13044577	chr20:25449835-25449836	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs560583760	chr20:25449836-25449837	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs13044860	chr20:25449851-25449852	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:56)

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
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
small cell lung cancer	20016488	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25425600-25453200	Weak transcription	Small Intestine	intestine
2	chr20:25426400-25450200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr20:25427200-25488200	Weak transcription	Stomach Mucosa	stomach
4	chr20:25429400-25463200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr20:25429800-25458800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr20:25430200-25484400	Strong transcription	Fetal Stomach	stomach
7	chr20:25431800-25484200	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr20:25432400-25450400	Strong transcription	Thymus	Thymus
9	chr20:25432600-25452400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr20:25434400-25460800	Weak transcription	Fetal Heart	heart
11	chr20:25435600-25459000	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr20:25435800-25450200	Weak transcription	Fetal Kidney	kidney
13	chr20:25435800-25465600	Weak transcription	NH-A	brain
14	chr20:25436200-25465200	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr20:25437800-25454600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr20:25438000-25450800	Strong transcription	Dnd41	blood
17	chr20:25438000-25452600	Strong transcription	Brain Germinal Matrix	brain
18	chr20:25438000-25456400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr20:25438200-25449200	Strong transcription	Liver	Liver
20	chr20:25438200-25449400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr20:25438200-25450200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr20:25438200-25452400	Strong transcription	Fetal Brain Female	brain
23	chr20:25438400-25451800	Strong transcription	Cortex derived primary cultured neurospheres	brain
24	chr20:25438400-25452600	Strong transcription	Ovary	ovary
25	chr20:25438400-25455400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr20:25438600-25451800	Strong transcription	Stomach Smooth Muscle	stomach
27	chr20:25438600-25453200	Strong transcription	Fetal Intestine Small	intestine
28	chr20:25438600-25466200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr20:25438800-25449200	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr20:25438800-25455000	Strong transcription	Fetal Intestine Large	intestine
31	chr20:25438800-25472600	Strong transcription	HepG2	liver
32	chr20:25440600-25466600	Weak transcription	Left Ventricle	heart
33	chr20:25441000-25452200	Strong transcription	A549	lung
34	chr20:25441200-25450200	Weak transcription	Colonic Mucosa	Colon
35	chr20:25441200-25450600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr20:25441800-25449400	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr20:25441800-25455000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr20:25442200-25460000	Weak transcription	Brain Angular Gyrus	brain
39	chr20:25442800-25450800	Weak transcription	Osteobl	bone
40	chr20:25443200-25459000	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr20:25443800-25457400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
42	chr20:25444000-25452000	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr20:25444200-25452600	Strong transcription	Duodenum Smooth Muscle	Duodenum
44	chr20:25444400-25450400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
45	chr20:25445000-25451400	Strong transcription	Gastric	stomach
46	chr20:25445200-25449400	Strong transcription	Fetal Thymus	thymus
47	chr20:25445200-25450800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr20:25445200-25451000	Strong transcription	Spleen	Spleen
49	chr20:25445200-25451200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr20:25445200-25451200	Strong transcription	Aorta	Aorta

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