Variant report

Variant	esv3323949
Chromosome Location	chr20:24467852-24472250
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	chr20:24458098..24460302-chr20:24472208..24475161,2	MCF-7	breast:
2	chr20:24462787..24464329-chr20:24469582..24472376,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CST7-5	chr20:24468399-24468664	NONHSAT079110
2	lnc-C20orf3-3	chr20:24472108-24472374	ENSG00000228539

Extended variants
information (count: 205 )
Associated
traits (count: 57 )

Variant overlapped rSNPs/rCNVs (count:205 , 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	rs567174300	chr20:24467957-24467958	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs537975530	chr20:24468000-24468001	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs144326169	chr20:24468024-24468025	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs527847146	chr20:24468032-24468033	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs186381945	chr20:24468034-24468035	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs376422108	chr20:24468057-24468058	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs540433679	chr20:24468115-24468116	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs6049726	chr20:24468152-24468153	Weak transcription Enhancers Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
9	rs6049727	chr20:24468156-24468157	Weak transcription Enhancers Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
10	rs546169147	chr20:24468161-24468162	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs139540978	chr20:24468180-24468181	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs539813178	chr20:24468188-24468189	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs35460384	chr20:24468194-24468195	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs189978974	chr20:24468205-24468206	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs115068521	chr20:24468222-24468223	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs561776423	chr20:24468223-24468224	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs6049728	chr20:24468238-24468239	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
18	rs115149016	chr20:24468248-24468249	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs180928558	chr20:24468258-24468259	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs557913521	chr20:24468283-24468284	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs368685521	chr20:24468370-24468371	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs6083535	chr20:24468403-24468404	Strong transcription Weak transcription Genic enhancers Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
23	rs535584752	chr20:24468449-24468450	Strong transcription Weak transcription Genic enhancers Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
24	rs185181436	chr20:24468468-24468469	Strong transcription Weak transcription Genic enhancers Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
25	rs533293848	chr20:24468477-24468478	Strong transcription Weak transcription Genic enhancers Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
26	rs80109724	chr20:24468507-24468508	Strong transcription Weak transcription Genic enhancers Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
27	rs370206782	chr20:24468515-24468516	Strong transcription Weak transcription Genic enhancers Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
28	rs8125671	chr20:24468536-24468537	Strong transcription Weak transcription Genic enhancers Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
29	rs568900019	chr20:24468577-24468578	Strong transcription Weak transcription Genic enhancers Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
30	rs554500628	chr20:24468578-24468579	Strong transcription Weak transcription Genic enhancers Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
31	rs372694170	chr20:24468611-24468612	Strong transcription Weak transcription Genic enhancers Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
32	rs147613948	chr20:24468657-24468658	Strong transcription Weak transcription Genic enhancers Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
33	rs6049729	chr20:24468686-24468687	Strong transcription Weak transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs189648287	chr20:24468714-24468715	Strong transcription Weak transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs73341677	chr20:24468745-24468746	Strong transcription Weak transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs546350924	chr20:24468760-24468761	Strong transcription Weak transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs556912234	chr20:24468777-24468778	Strong transcription Weak transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs10627332	chr20:24468796-24468797	Strong transcription Weak transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs33929780	chr20:24468797-24468798	Strong transcription Weak transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs386393567	chr20:24468799-24468800	Strong transcription Weak transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs199614986	chr20:24468801-24468802	Strong transcription Weak transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs200706100	chr20:24468802-24468803	Strong transcription Weak transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs11283374	chr20:24468803-24468804	Strong transcription Weak transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs576770447	chr20:24468829-24468830	Strong transcription Weak transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs143166689	chr20:24468870-24468871	Strong transcription Weak transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs561666586	chr20:24468919-24468920	Strong transcription Weak transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs184063587	chr20:24468923-24468924	Strong transcription Weak transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs540756146	chr20:24468925-24468926	Strong transcription Weak transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs374811231	chr20:24468927-24468928	Strong transcription Weak transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs114515201	chr20:24468971-24468972	Strong transcription Weak transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:57)

Disease	PMID	Source
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
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
Cancer	20164919	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:136 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24457600-24470600	Weak transcription	Fetal Brain Female	brain
2	chr20:24459400-24471000	Weak transcription	Fetal Muscle Leg	muscle
3	chr20:24459400-24471800	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr20:24459600-24472000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr20:24460200-24468800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr20:24460200-24469600	Weak transcription	Brain Anterior Caudate	brain
7	chr20:24460200-24471400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr20:24460200-24472600	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr20:24460400-24468200	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr20:24460400-24468600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr20:24460400-24469600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr20:24460800-24468400	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr20:24460800-24469800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr20:24460800-24483800	Weak transcription	Aorta	Aorta
15	chr20:24461400-24468200	Weak transcription	Brain Cingulate Gyrus	brain
16	chr20:24461400-24469800	Weak transcription	Fetal Brain Male	brain
17	chr20:24461600-24468000	Weak transcription	Brain Angular Gyrus	brain
18	chr20:24461800-24468600	Weak transcription	Brain Substantia Nigra	brain
19	chr20:24462200-24469000	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr20:24462400-24469800	Weak transcription	Fetal Kidney	kidney
21	chr20:24462400-24472600	Weak transcription	Right Atrium	heart
22	chr20:24463200-24469600	Weak transcription	Fetal Lung	lung
23	chr20:24464600-24468000	Weak transcription	Brain Hippocampus Middle	brain
24	chr20:24464600-24472000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr20:24465000-24472800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr20:24465200-24469800	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr20:24465200-24469800	Weak transcription	Gastric	stomach
28	chr20:24465600-24468200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr20:24466000-24468200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr20:24466400-24469400	Weak transcription	Brain Germinal Matrix	brain
31	chr20:24466600-24469800	Enhancers	Fetal Heart	heart
32	chr20:24466800-24469000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr20:24467000-24469800	Weak transcription	Right Ventricle	heart
34	chr20:24467600-24472800	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr20:24468000-24468400	Enhancers	Brain Angular Gyrus	brain
36	chr20:24468000-24468400	Strong transcription	Brain Hippocampus Middle	brain
37	chr20:24468000-24468600	Enhancers	Left Ventricle	heart
38	chr20:24468200-24470000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr20:24468200-24470400	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr20:24468200-24470400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
41	chr20:24468200-24470400	Genic enhancers	Brain Cingulate Gyrus	brain
42	chr20:24468400-24469200	Genic enhancers	Brain Hippocampus Middle	brain
43	chr20:24468400-24469400	Enhancers	Colonic Mucosa	Colon
44	chr20:24468400-24469400	Enhancers	Sigmoid Colon	Sigmoid Colon
45	chr20:24468400-24469800	Weak transcription	Brain Angular Gyrus	brain
46	chr20:24468400-24470200	Enhancers	Rectal Mucosa Donor 31	rectum
47	chr20:24468400-24470400	Strong transcription	H1 Cell Line	embryonic stem cell
48	chr20:24468600-24469000	Genic enhancers	Brain Substantia Nigra	brain
49	chr20:24468600-24469200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr20:24468600-24470000	Weak transcription	Left Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links