Variant report

Variant	nsv459100
Chromosome Location	chr21:17777966-17826260
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BRCA1	chr21:17791560-17792044	Hela-S3	cervix:	n/a	n/a
2	CCNT2	chr21:17793344-17793475	K562	blood:	n/a	n/a
3	CEBPB	chr21:17796273-17796481	Hela-S3	cervix:	n/a	chr21:17796368-17796379 chr21:17796366-17796379
4	CEBPB	chr21:17797768-17798408	Hela-S3	cervix:	n/a	n/a
5	CEBPB	chr21:17792425-17792909	Hela-S3	cervix:	n/a	n/a
6	CEBPB	chr21:17792367-17792742	ECC-1	luminal epithelium:	n/a	chr21:17792377-17792386
7	CEBPB	chr21:17794875-17795400	Hela-S3	cervix:	n/a	chr21:17794990-17795001 chr21:17794990-17795003
8	CEBPB	chr21:17818801-17819060	HepG2	liver:	n/a	chr21:17818924-17818935
9	CHD2	chr21:17791479-17792210	Hela-S3	cervix:	n/a	n/a
10	CTCF	chr21:17780220-17780370	HUVEC	blood vessel:	n/a	n/a
11	CTCF	chr21:17789614-17789790	Medullo	brain:	n/a	n/a
12	CTCF	chr21:17800537-17800627	Kidney_OC	kidney:	n/a	n/a
13	E2F4	chr21:17792581-17792835	MCF10A-Er-Src	breast:	n/a	n/a
14	E2F4	chr21:17791301-17791451	MCF10A-Er-Src	breast:	n/a	n/a
15	E2F4	chr21:17799768-17799938	MCF10A-Er-Src	breast:	n/a	n/a
16	ELF1	chr21:17791233-17791845	MCF-7	breast:	n/a	n/a
17	ELF1	chr21:17791357-17791669	HepG2	liver:	n/a	n/a
18	EP300	chr21:17791466-17791843	SK-N-SH_RA	brain:	n/a	chr21:17791596-17791606
19	EP300	chr21:17797155-17799919	SK-N-SH	brain:	n/a	chr21:17797369-17797378
20	EP300	chr21:17792320-17792861	Hela-S3	cervix:	n/a	n/a
21	EP300	chr21:17798156-17798429	SK-N-SH_RA	brain:	n/a	n/a
22	EP300	chr21:17780136-17780389	SK-N-SH_RA	brain:	n/a	chr21:17780282-17780296
23	EP300	chr21:17792230-17793023	ECC-1	luminal epithelium:	n/a	n/a
24	EP300	chr21:17791394-17791805	SK-N-SH_RA	brain:	n/a	chr21:17791596-17791606
25	EP300	chr21:17797663-17798260	Hela-S3	cervix:	n/a	n/a
26	EP300	chr21:17792345-17792885	ECC-1	luminal epithelium:	n/a	n/a
27	EP300	chr21:17792447-17792711	SK-N-SH_RA	brain:	n/a	n/a
28	EP300	chr21:17799814-17800446	ECC-1	luminal epithelium:	n/a	chr21:17799971-17799985 chr21:17799978-17799992 chr21:17799968-17799982 chr21:17799970-17799984 chr21:17799969-17799983 chr21:17799972-17799986
29	EP300	chr21:17826072-17826076	GM12878	blood:	n/a	n/a
30	ESR1	chr21:17803565-17803786	ECC-1	luminal epithelium:	n/a	n/a
31	ESR1	chr21:17792410-17792831	ECC-1	luminal epithelium:	n/a	chr21:17792723-17792740
32	ESR1	chr21:17803396-17803834	ECC-1	luminal epithelium:	n/a	n/a
33	ESR1	chr21:17800738-17801435	ECC-1	luminal epithelium:	n/a	chr21:17800982-17800999 chr21:17800983-17801000
34	ESR1	chr21:17800801-17801392	ECC-1	luminal epithelium:	n/a	chr21:17800982-17800999 chr21:17800983-17801000
35	ESR1	chr21:17792349-17792958	ECC-1	luminal epithelium:	n/a	chr21:17792723-17792740
36	ESR1	chr21:17800643-17801437	ECC-1	luminal epithelium:	n/a	chr21:17800982-17800999 chr21:17800983-17801000
37	ESR1	chr21:17803418-17803879	ECC-1	luminal epithelium:	n/a	n/a
38	ESR1	chr21:17803443-17803867	ECC-1	luminal epithelium:	n/a	n/a
39	ESR1	chr21:17800724-17801392	ECC-1	luminal epithelium:	n/a	chr21:17800982-17800999 chr21:17800983-17801000
40	ESR1	chr21:17800843-17801192	ECC-1	luminal epithelium:	n/a	chr21:17800982-17800999 chr21:17800983-17801000
41	ESR1	chr21:17792414-17792864	ECC-1	luminal epithelium:	n/a	chr21:17792723-17792740
42	FOS	chr21:17797602-17798217	HUVEC	blood vessel:	n/a	n/a
43	FOS	chr21:17796729-17797285	HUVEC	blood vessel:	n/a	chr21:17797059-17797069
44	FOS	chr21:17818346-17818632	MCF10A-Er-Src	breast:	n/a	n/a
45	FOS	chr21:17798165-17798330	MCF10A-Er-Src	breast:	n/a	n/a
46	FOS	chr21:17818346-17818656	MCF10A-Er-Src	breast:	n/a	n/a
47	FOS	chr21:17818869-17819102	MCF10A-Er-Src	breast:	n/a	n/a
48	FOS	chr21:17818346-17818635	MCF10A-Er-Src	breast:	n/a	n/a
49	FOS	chr21:17798152-17798305	MCF10A-Er-Src	breast:	n/a	n/a
50	FOS	chr21:17818869-17819045	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr21:17789969..17792696-chr21:17799605..17801790,2	MCF-7	breast:
2	chr21:17795082..17798298-chr21:17801061..17804757,3	MCF-7	breast:
3	chr21:17812930..17814449-chr21:17824658..17826257,2	MCF-7	breast:
4	chr21:17802778..17805125-chr21:17808909..17810799,2	MCF-7	breast:
5	chr21:17793428..17795619-chr21:17796309..17799030,2	MCF-7	breast:
6	chr21:17787241..17789813-chr21:17791382..17794099,2	K562	blood:
7	chr21:17793428..17795619-chr21:17796309..17799030,2	MCF-7	breast:
8	chr21:17802778..17805125-chr21:17808909..17810799,2	MCF-7	breast:
9	chr21:17812930..17814449-chr21:17824658..17826257,2	MCF-7	breast:
10	chr21:17795082..17798298-chr21:17801061..17804757,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-USP25-2	chr21:17792775-17792892	ENSG00000215386.6
2	lnc-BTG3-12	chr21:17789459-17789778	ENSG00000270139.1
3	lnc-BTG3-12	chr21:17791179-17791281	ENSG00000270139.1
4	lnc-USP25-2	chr21:17791716-17792061	NONHSAT081235
5	lnc-USP25-2	chr21:17791722-17792061	ENSG00000215386.6
6	lnc-BTG3-12	chr21:17791357-17791400	ENSG00000270139.1
7	lnc-USP25-2	chr21:17791752-17792061	ENSG00000215386
8	lnc-USP25-2	chr21:17791593-17792061	XLOC_013868
9	lnc-USP25-2	chr21:17791648-17792061	ENSG00000215386.6
10	lnc-USP25-2	chr21:17791999-17792061	ENSG00000215386
11	lnc-USP25-2	chr21:17791838-17792061	ENSG00000215386

Variant related genes	Relation type
ENSG00000270139	TF binding region
LINC00478	TF binding region
ENSG00000270139	chromatin interactions
ENSG00000215386	chromatin interactions
COX7A2L	miRNA target sites
RNF145	miRNA target sites
CAMTA1	miRNA target sites

Extended variants
information (count: 2020 )
Associated
traits (count: 72 )

Variant overlapped rSNPs/rCNVs (count:2020 , 50 per page) page: 1 2 3 4 5 6 7 ... 41

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs2823785	chr21:17777966-17777967	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs1034342	chr21:17778027-17778028	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
3	rs140833276	chr21:17778106-17778107	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs542297170	chr21:17778168-17778169	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs562162687	chr21:17778218-17778219	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs1034343	chr21:17778226-17778227	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs550735243	chr21:17778238-17778239	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs564251018	chr21:17778242-17778243	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs191967591	chr21:17778256-17778257	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs552699928	chr21:17778257-17778258	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs546293351	chr21:17778310-17778311	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs566088399	chr21:17778318-17778319	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs116236438	chr21:17778332-17778333	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs9983206	chr21:17778333-17778334	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs568600018	chr21:17778357-17778358	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs538266038	chr21:17778362-17778363	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs1034344	chr21:17778366-17778367	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
18	rs185566183	chr21:17778381-17778382	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs577485824	chr21:17778390-17778391	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs190474141	chr21:17778435-17778436	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs371845802	chr21:17778442-17778443	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs377183138	chr21:17778456-17778457	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs540088376	chr21:17778471-17778472	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs79542728	chr21:17778508-17778509	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs573322339	chr21:17778519-17778520	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs574032596	chr21:17778526-17778527	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs542235997	chr21:17778571-17778572	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs555932668	chr21:17778594-17778595	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs575785250	chr21:17778614-17778615	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs78011764	chr21:17778698-17778699	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs536500091	chr21:17778709-17778710	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs375492138	chr21:17778735-17778736	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs564273017	chr21:17778749-17778750	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs369566604	chr21:17778752-17778753	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs138298530	chr21:17778780-17778781	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs540471432	chr21:17778852-17778853	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs556094687	chr21:17778858-17778859	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs544462046	chr21:17778873-17778874	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs141016675	chr21:17778909-17778910	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs528896103	chr21:17778966-17778967	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs75021007	chr21:17779085-17779086	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs377085868	chr21:17779089-17779090	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs150338703	chr21:17779114-17779115	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs531403221	chr21:17779150-17779151	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs138035573	chr21:17779158-17779159	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs570980999	chr21:17779171-17779172	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs76708687	chr21:17779176-17779177	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs149528308	chr21:17779194-17779195	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs540418770	chr21:17779210-17779211	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs116763494	chr21:17779223-17779224	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:72)

Disease	PMID	Source
Ovarian cancer	21720365	CNVD
Wilms tumour	21544195	CNVD
Esophageal cancer	21851588	CNVD
Glioblastoma multiforme	21080181	CNVD
Cancer	16751803	CNVD
Medulloblastoma	21979893	CNVD
Pleomorphic xanthoastrocytoma	20730472	CNVD
Down syndrome	17412756	CNVD
Down syndrome	17576883	CNVD
Acute promyelocytic leukemia	19109227	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Autism	22495311	CNVD
Lung cancer	18438408	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute myeloid leukemia	20729466	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
T-cell lymphomas	19863542	CNVD
Non-small cell lung cancer	21044232	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Astrocytoma	17387387	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	17387387	CNVD
Renal cell carcinoma	19461508	CNVD
Seminomas	18059402	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
Metanephric adenoma	20802469	CNVD
Neuroblastoma	18923191	CNVD
Prostate cancer	19156837	CNVD
Basal cell lymphoma	17170743	CNVD
Follicular lymphoma	17170743	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Cancer	20164919	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
lymphocytic leukemia	21291569	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Acute myeloid leukemia	21251322	CNVD
abnormal development	18461090	CNVD
Breast cancer	21785460	CNVD
Breast cancer	21364760	CNVD
Multiple myeloma	17550852	CNVD
Myelofibrosis	22110671	CNVD
Alzheimer''s disease	18923514	CNVD
Alzheimer''s disease	20877625	CNVD
Follicular lymphoma	20505157	CNVD
Alzheimer''s disease	21956041	CNVD
Cancer	21183584	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
Melanoma	18172304	CNVD
Autism	22958593	CNVD
Schizophrenia	22958593	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Lung cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Epilepsy	20502679	CNVD
22q11.2 microdeletion syndrome	19750312	CNVD
Breast cancer	20409316	CNVD
Gastric cancer	18160780	CNVD
Medullary thyroid carcinoma	18765511	CNVD
Breast cancer	22522925	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD
Pancreatic cancer	17952125	CNVD
T-cell lymphomas	22341440	CNVD

Chromatin state (count:524 , 50 per page) page: 1 2 3 4 5 6 7 ... 11

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:17761600-17780200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr21:17771400-17791200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr21:17775400-17782200	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr21:17775400-17786600	Weak transcription	Ovary	ovary
5	chr21:17775600-17786000	Weak transcription	Brain Anterior Caudate	brain
6	chr21:17775800-17782000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr21:17776800-17778400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr21:17777600-17778800	Weak transcription	Adipose Nuclei	Adipose
9	chr21:17778200-17780000	Enhancers	Liver	Liver
10	chr21:17778800-17779000	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr21:17778800-17779000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr21:17778800-17779000	Enhancers	Adipose Nuclei	Adipose
13	chr21:17778800-17779000	Enhancers	Psoas Muscle	Psoas
14	chr21:17778800-17779000	Enhancers	Right Atrium	heart
15	chr21:17779000-17780200	Weak transcription	Psoas Muscle	Psoas
16	chr21:17779000-17782000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr21:17779200-17780200	Weak transcription	Right Atrium	heart
18	chr21:17780000-17780200	Enhancers	Osteobl	bone
19	chr21:17780000-17780800	Flanking Active TSS	Liver	Liver
20	chr21:17780200-17780400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr21:17780200-17780600	Enhancers	Fetal Heart	heart
22	chr21:17780200-17780600	Enhancers	Psoas Muscle	Psoas
23	chr21:17780200-17780600	Enhancers	Right Atrium	heart
24	chr21:17780200-17780600	Flanking Active TSS	Osteobl	bone
25	chr21:17780200-17781000	Enhancers	Muscle Satellite Cultured Cells	--
26	chr21:17780200-17781200	Enhancers	NH-A	brain
27	chr21:17780400-17781000	Enhancers	Fetal Lung	lung
28	chr21:17780400-17781200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr21:17780600-17781200	Enhancers	Osteobl	bone
30	chr21:17780800-17781000	Enhancers	Liver	Liver
31	chr21:17781000-17789600	Weak transcription	Liver	Liver
32	chr21:17781200-17790400	Weak transcription	NH-A	brain
33	chr21:17782000-17782200	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr21:17786000-17786200	Enhancers	Brain Inferior Temporal Lobe	brain
35	chr21:17786000-17786800	Enhancers	Brain Anterior Caudate	brain
36	chr21:17786200-17788200	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr21:17786600-17786800	Active TSS	Ovary	ovary
38	chr21:17786800-17788200	Weak transcription	Ovary	ovary
39	chr21:17786800-17789200	Weak transcription	Brain Anterior Caudate	brain
40	chr21:17788200-17788400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
41	chr21:17788200-17788400	Enhancers	Right Atrium	heart
42	chr21:17788200-17788600	Enhancers	Brain Angular Gyrus	brain
43	chr21:17788200-17788600	Enhancers	Brain Inferior Temporal Lobe	brain
44	chr21:17788200-17788800	Enhancers	Ovary	ovary
45	chr21:17788400-17790600	Weak transcription	Right Atrium	heart
46	chr21:17788400-17790800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr21:17788600-17790400	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr21:17788600-17790600	Weak transcription	Brain Angular Gyrus	brain
49	chr21:17788800-17791000	Weak transcription	Ovary	ovary
50	chr21:17789200-17789400	Weak transcription	Cortex derived primary cultured neurospheres	brain

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