Variant report

Variant	nsv979406
Chromosome Location	chr20:25509600-25513942
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:25508566..25510611-chr20:25564676..25566360,2	MCF-7	breast:
2	chr20:25499922..25502486-chr20:25510143..25513350,3	MCF-7	breast:
3	chr20:25504894..25507358-chr20:25508312..25510600,2	MCF-7	breast:
4	chr20:25512408..25515336-chr20:25515482..25519858,3	MCF-7	breast:
5	chr20:25371156..25372734-chr20:25509417..25511739,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GINS1-4	chr20:25513663-25514148	NONHSAT079162

Variant related genes	Relation type
ENSG00000101004	chromatin interactions
ENSG00000100997	chromatin interactions

Extended variants
information (count: 230 )
Associated
traits (count: 56 )

Variant overlapped rSNPs/rCNVs (count:230 , 50 per page) page: 1 2 3 4 5

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs73335402	chr20:25509603-25509604	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs6138595	chr20:25509632-25509633	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
3	rs547267371	chr20:25509633-25509634	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
4	rs400070	chr20:25509638-25509639	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
5	rs539000718	chr20:25509652-25509653	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
6	rs182203922	chr20:25509653-25509654	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
7	rs73337303	chr20:25509666-25509667	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
8	rs575794952	chr20:25509691-25509692	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
9	rs543529677	chr20:25509697-25509698	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
10	rs538334109	chr20:25509704-25509705	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
11	rs141503395	chr20:25509765-25509766	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs574255215	chr20:25509787-25509788	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
13	rs533743659	chr20:25509847-25509848	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
14	rs115595056	chr20:25509867-25509868	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
15	rs187240741	chr20:25509903-25509904	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
16	rs146222579	chr20:25509989-25509990	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
17	rs79060758	chr20:25510030-25510031	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
18	rs190120516	chr20:25510069-25510070	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
19	rs6037133	chr20:25510101-25510102	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
20	rs530288607	chr20:25510127-25510128	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
21	rs11467046	chr20:25510141-25510142	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
22	rs71332658	chr20:25510144-25510145	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
23	rs368939643	chr20:25510145-25510146	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
24	rs372281131	chr20:25510146-25510147	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
25	rs376611249	chr20:25510147-25510148	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
26	rs116519462	chr20:25510178-25510179	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
27	rs4813570	chr20:25510179-25510180	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
28	rs111714812	chr20:25510225-25510226	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
29	rs552643232	chr20:25510230-25510231	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
30	rs569228018	chr20:25510239-25510240	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
31	rs376135562	chr20:25510248-25510249	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
32	rs201731294	chr20:25510254-25510255	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
33	rs537863227	chr20:25510276-25510277	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
34	rs541067005	chr20:25510290-25510291	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
35	rs181737940	chr20:25510304-25510305	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
36	rs148004040	chr20:25510329-25510330	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
37	rs553525921	chr20:25510332-25510333	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
38	rs369598265	chr20:25510357-25510358	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
39	rs6037134	chr20:25510438-25510439	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
40	rs561535131	chr20:25510467-25510468	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
41	rs141756669	chr20:25510472-25510473	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
42	rs530451762	chr20:25510478-25510479	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
43	rs79106713	chr20:25510502-25510503	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
44	rs548585472	chr20:25510514-25510515	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
45	rs556192834	chr20:25510582-25510583	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
46	rs150561053	chr20:25510678-25510679	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs139543437	chr20:25510684-25510685	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
48	rs555405837	chr20:25510727-25510728	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
49	rs572157204	chr20:25510728-25510729	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
50	rs144525108	chr20:25510775-25510776	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	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:213 , 50 per page) page: 1 2 3 4 5

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25493200-25512800	Weak transcription	Colon Smooth Muscle	Colon
2	chr20:25493600-25513000	Weak transcription	Left Ventricle	heart
3	chr20:25495800-25519400	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr20:25496000-25512400	Weak transcription	Brain Angular Gyrus	brain
5	chr20:25496000-25513200	Weak transcription	HUVEC	blood vessel
6	chr20:25497400-25512400	Weak transcription	Brain Cingulate Gyrus	brain
7	chr20:25497400-25512400	Weak transcription	Rectal Smooth Muscle	rectum
8	chr20:25497400-25514800	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr20:25497600-25512600	Weak transcription	Fetal Heart	heart
10	chr20:25497800-25512200	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr20:25498000-25511000	Weak transcription	Brain Hippocampus Middle	brain
12	chr20:25498200-25510800	Weak transcription	Brain Substantia Nigra	brain
13	chr20:25498200-25512200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr20:25498200-25512200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr20:25498200-25512600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr20:25498200-25512600	Weak transcription	Brain Anterior Caudate	brain
17	chr20:25498200-25512800	Weak transcription	Adipose Nuclei	Adipose
18	chr20:25498200-25513000	Weak transcription	Fetal Thymus	thymus
19	chr20:25498200-25514600	Weak transcription	Pancreas	Pancrea
20	chr20:25498200-25519000	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr20:25498200-25519400	Weak transcription	Gastric	stomach
22	chr20:25498200-25532200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr20:25498400-25519200	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr20:25498600-25512800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr20:25502600-25519800	Weak transcription	Stomach Mucosa	stomach
26	chr20:25502800-25513200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr20:25503400-25512400	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr20:25504800-25512800	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr20:25505000-25512800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr20:25505200-25512800	Weak transcription	Esophagus	oesophagus
31	chr20:25505200-25513800	Weak transcription	Fetal Kidney	kidney
32	chr20:25505400-25513000	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr20:25505400-25514600	Weak transcription	Lung	lung
34	chr20:25505400-25521000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr20:25507000-25510600	Weak transcription	Fetal Brain Male	brain
36	chr20:25507000-25512800	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr20:25507200-25510800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr20:25507200-25512200	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr20:25507200-25512400	Weak transcription	Stomach Smooth Muscle	stomach
40	chr20:25507200-25512600	Weak transcription	Fetal Muscle Leg	muscle
41	chr20:25507200-25513400	Weak transcription	Fetal Lung	lung
42	chr20:25507400-25510600	Weak transcription	Fetal Brain Female	brain
43	chr20:25507400-25510800	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr20:25507400-25512200	Weak transcription	Thymus	Thymus
45	chr20:25507400-25512200	Weak transcription	Spleen	Spleen
46	chr20:25507400-25512400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr20:25507400-25512400	Weak transcription	Fetal Muscle Trunk	muscle
48	chr20:25507400-25512600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr20:25507400-25512600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr20:25507400-25512800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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