Variant report

Variant	nsv913419
Chromosome Location	chr21:17775056-17826260
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	chr21:17794875-17795400	Hela-S3	cervix:	n/a	chr21:17794990-17795001 chr21:17794990-17795003
4	CEBPB	chr21:17796273-17796481	Hela-S3	cervix:	n/a	chr21:17796368-17796379 chr21:17796366-17796379
5	CEBPB	chr21:17792367-17792742	ECC-1	luminal epithelium:	n/a	chr21:17792377-17792386
6	CEBPB	chr21:17792425-17792909	Hela-S3	cervix:	n/a	n/a
7	CEBPB	chr21:17797768-17798408	Hela-S3	cervix:	n/a	n/a
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	chr21:17800537-17800627	Kidney_OC	kidney:	n/a	n/a
12	CTCF	chr21:17789614-17789790	Medullo	brain:	n/a	n/a
13	E2F4	chr21:17792581-17792835	MCF10A-Er-Src	breast:	n/a	n/a
14	E2F4	chr21:17799768-17799938	MCF10A-Er-Src	breast:	n/a	n/a
15	E2F4	chr21:17791301-17791451	MCF10A-Er-Src	breast:	n/a	n/a
16	ELF1	chr21:17791357-17791669	HepG2	liver:	n/a	n/a
17	ELF1	chr21:17791233-17791845	MCF-7	breast:	n/a	n/a
18	EP300	chr21:17792345-17792885	ECC-1	luminal epithelium:	n/a	n/a
19	EP300	chr21:17792447-17792711	SK-N-SH_RA	brain:	n/a	n/a
20	EP300	chr21:17791466-17791843	SK-N-SH_RA	brain:	n/a	chr21:17791596-17791606
21	EP300	chr21:17797155-17799919	SK-N-SH	brain:	n/a	chr21:17797369-17797378
22	EP300	chr21:17798156-17798429	SK-N-SH_RA	brain:	n/a	n/a
23	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
24	EP300	chr21:17797663-17798260	Hela-S3	cervix:	n/a	n/a
25	EP300	chr21:17780136-17780389	SK-N-SH_RA	brain:	n/a	chr21:17780282-17780296
26	EP300	chr21:17791394-17791805	SK-N-SH_RA	brain:	n/a	chr21:17791596-17791606
27	EP300	chr21:17792320-17792861	Hela-S3	cervix:	n/a	n/a
28	EP300	chr21:17826072-17826076	GM12878	blood:	n/a	n/a
29	EP300	chr21:17792230-17793023	ECC-1	luminal epithelium:	n/a	n/a
30	ESR1	chr21:17803418-17803879	ECC-1	luminal epithelium:	n/a	n/a
31	ESR1	chr21:17800843-17801192	ECC-1	luminal epithelium:	n/a	chr21:17800982-17800999 chr21:17800983-17801000
32	ESR1	chr21:17792414-17792864	ECC-1	luminal epithelium:	n/a	chr21:17792723-17792740
33	ESR1	chr21:17803396-17803834	ECC-1	luminal epithelium:	n/a	n/a
34	ESR1	chr21:17800801-17801392	ECC-1	luminal epithelium:	n/a	chr21:17800982-17800999 chr21:17800983-17801000
35	ESR1	chr21:17800643-17801437	ECC-1	luminal epithelium:	n/a	chr21:17800982-17800999 chr21:17800983-17801000
36	ESR1	chr21:17792410-17792831	ECC-1	luminal epithelium:	n/a	chr21:17792723-17792740
37	ESR1	chr21:17803565-17803786	ECC-1	luminal epithelium:	n/a	n/a
38	ESR1	chr21:17800738-17801435	ECC-1	luminal epithelium:	n/a	chr21:17800982-17800999 chr21:17800983-17801000
39	ESR1	chr21:17800724-17801392	ECC-1	luminal epithelium:	n/a	chr21:17800982-17800999 chr21:17800983-17801000
40	ESR1	chr21:17792349-17792958	ECC-1	luminal epithelium:	n/a	chr21:17792723-17792740
41	ESR1	chr21:17803443-17803867	ECC-1	luminal epithelium:	n/a	n/a
42	FOS	chr21:17776101-17776160	MCF10A-Er-Src	breast:	n/a	n/a
43	FOS	chr21:17796729-17797285	HUVEC	blood vessel:	n/a	chr21:17797059-17797069
44	FOS	chr21:17818346-17818635	MCF10A-Er-Src	breast:	n/a	n/a
45	FOS	chr21:17798152-17798305	MCF10A-Er-Src	breast:	n/a	n/a
46	FOS	chr21:17818869-17819045	MCF10A-Er-Src	breast:	n/a	n/a
47	FOS	chr21:17818346-17818656	MCF10A-Er-Src	breast:	n/a	n/a
48	FOS	chr21:17798165-17798330	MCF10A-Er-Src	breast:	n/a	n/a
49	FOS	chr21:17818869-17819102	MCF10A-Er-Src	breast:	n/a	n/a
50	FOS	chr21:17818346-17818632	MCF10A-Er-Src	breast:	n/a	n/a

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

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

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

Extended variants
information (count: 2137 )
Associated
traits (count: 72 )

Variant overlapped rSNPs/rCNVs (count:2137 , 50 per page) page: 1 2 3 4 5 6 7 ... 43

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs1900938	chr21:17775056-17775057	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs8127615	chr21:17775119-17775120	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs186017094	chr21:17775165-17775166	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs531025576	chr21:17775204-17775205	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs9978348	chr21:17775206-17775207	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
6	rs8131137	chr21:17775226-17775227	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs547787285	chr21:17775261-17775262	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs530661333	chr21:17775265-17775266	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs240491	chr21:17775267-17775268	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
10	rs536350599	chr21:17775280-17775281	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs240492	chr21:17775303-17775304	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
12	rs533461369	chr21:17775318-17775319	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs569805737	chr21:17775329-17775330	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs538859808	chr21:17775345-17775346	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs35220980	chr21:17775363-17775364	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs558443805	chr21:17775408-17775409	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs572324601	chr21:17775431-17775432	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs200409188	chr21:17775503-17775504	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs2167060	chr21:17775518-17775519	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
20	rs554612101	chr21:17775533-17775534	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs73177635	chr21:17775558-17775559	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
22	rs114599431	chr21:17775582-17775583	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs191178231	chr21:17775584-17775585	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs118119351	chr21:17775611-17775612	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs75551406	chr21:17775644-17775645	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs75574889	chr21:17775654-17775655	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs28838378	chr21:17775672-17775673	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs58056075	chr21:17775675-17775676	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs2155840	chr21:17775687-17775688	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
30	rs565304262	chr21:17775690-17775691	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs527998235	chr21:17775713-17775714	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs368274009	chr21:17775757-17775758	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs535990418	chr21:17775773-17775774	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs568904320	chr21:17775814-17775815	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs561242168	chr21:17775815-17775816	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs530076871	chr21:17775902-17775903	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs183452904	chr21:17775930-17775931	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs375270167	chr21:17775933-17775934	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs188954361	chr21:17775941-17775942	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs532470513	chr21:17775960-17775961	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs552362908	chr21:17775969-17775970	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs192345917	chr21:17775980-17775981	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs534917966	chr21:17776038-17776039	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs35732759	chr21:17776133-17776134	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs554946837	chr21:17776155-17776156	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs568349940	chr21:17776157-17776158	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs140316165	chr21:17776158-17776159	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs62216391	chr21:17776168-17776169	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
49	rs74514379	chr21:17776198-17776199	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs12627693	chr21:17776199-17776200	Weak transcription	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:543 , 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	chr21:17770000-17775200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr21:17771000-17775400	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr21:17771400-17791200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr21:17774800-17775400	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr21:17775000-17775400	Enhancers	Brain Angular Gyrus	brain
7	chr21:17775000-17775400	Enhancers	Ovary	ovary
8	chr21:17775000-17775600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr21:17775000-17775600	Enhancers	Brain Anterior Caudate	brain
10	chr21:17775000-17775600	Enhancers	Brain Cingulate Gyrus	brain
11	chr21:17775000-17775600	Enhancers	Brain Substantia Nigra	brain
12	chr21:17775000-17775600	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr21:17775000-17775800	Enhancers	Left Ventricle	heart
14	chr21:17775200-17775400	Enhancers	Adipose Nuclei	Adipose
15	chr21:17775200-17775600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr21:17775400-17782200	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr21:17775400-17786600	Weak transcription	Ovary	ovary
18	chr21:17775600-17776800	Weak transcription	Adipose Nuclei	Adipose
19	chr21:17775600-17786000	Weak transcription	Brain Anterior Caudate	brain
20	chr21:17775800-17782000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr21:17776800-17777600	Enhancers	Adipose Nuclei	Adipose
22	chr21:17776800-17778400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr21:17777000-17777200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr21:17777000-17777600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr21:17777200-17777600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr21:17777600-17777800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr21:17777600-17778800	Weak transcription	Adipose Nuclei	Adipose
28	chr21:17778200-17780000	Enhancers	Liver	Liver
29	chr21:17778800-17779000	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr21:17778800-17779000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr21:17778800-17779000	Enhancers	Adipose Nuclei	Adipose
32	chr21:17778800-17779000	Enhancers	Psoas Muscle	Psoas
33	chr21:17778800-17779000	Enhancers	Right Atrium	heart
34	chr21:17779000-17780200	Weak transcription	Psoas Muscle	Psoas
35	chr21:17779000-17782000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr21:17779200-17780200	Weak transcription	Right Atrium	heart
37	chr21:17780000-17780200	Enhancers	Osteobl	bone
38	chr21:17780000-17780800	Flanking Active TSS	Liver	Liver
39	chr21:17780200-17780400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr21:17780200-17780600	Enhancers	Fetal Heart	heart
41	chr21:17780200-17780600	Enhancers	Psoas Muscle	Psoas
42	chr21:17780200-17780600	Enhancers	Right Atrium	heart
43	chr21:17780200-17780600	Flanking Active TSS	Osteobl	bone
44	chr21:17780200-17781000	Enhancers	Muscle Satellite Cultured Cells	--
45	chr21:17780200-17781200	Enhancers	NH-A	brain
46	chr21:17780400-17781000	Enhancers	Fetal Lung	lung
47	chr21:17780400-17781200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr21:17780600-17781200	Enhancers	Osteobl	bone
49	chr21:17780800-17781000	Enhancers	Liver	Liver
50	chr21:17781000-17789600	Weak transcription	Liver	Liver

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