Variant report

Variant	nsv913421
Chromosome Location	chr21:17786219-17826260
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	chr21:17792425-17792909	Hela-S3	cervix:	n/a	n/a
4	CEBPB	chr21:17818801-17819060	HepG2	liver:	n/a	chr21:17818924-17818935
5	CEBPB	chr21:17797768-17798408	Hela-S3	cervix:	n/a	n/a
6	CEBPB	chr21:17796273-17796481	Hela-S3	cervix:	n/a	chr21:17796368-17796379 chr21:17796366-17796379
7	CEBPB	chr21:17794875-17795400	Hela-S3	cervix:	n/a	chr21:17794990-17795001 chr21:17794990-17795003
8	CEBPB	chr21:17792367-17792742	ECC-1	luminal epithelium:	n/a	chr21:17792377-17792386
9	CHD2	chr21:17791479-17792210	Hela-S3	cervix:	n/a	n/a
10	CTCF	chr21:17800537-17800627	Kidney_OC	kidney:	n/a	n/a
11	CTCF	chr21:17789614-17789790	Medullo	brain:	n/a	n/a
12	E2F4	chr21:17791301-17791451	MCF10A-Er-Src	breast:	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	ELF1	chr21:17791233-17791845	MCF-7	breast:	n/a	n/a
16	ELF1	chr21:17791357-17791669	HepG2	liver:	n/a	n/a
17	EP300	chr21:17791466-17791843	SK-N-SH_RA	brain:	n/a	chr21:17791596-17791606
18	EP300	chr21:17792320-17792861	Hela-S3	cervix:	n/a	n/a
19	EP300	chr21:17797155-17799919	SK-N-SH	brain:	n/a	chr21:17797369-17797378
20	EP300	chr21:17792345-17792885	ECC-1	luminal epithelium:	n/a	n/a
21	EP300	chr21:17798156-17798429	SK-N-SH_RA	brain:	n/a	n/a
22	EP300	chr21:17791394-17791805	SK-N-SH_RA	brain:	n/a	chr21:17791596-17791606
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	chr21:17792230-17793023	ECC-1	luminal epithelium:	n/a	n/a
25	EP300	chr21:17826072-17826076	GM12878	blood:	n/a	n/a
26	EP300	chr21:17797663-17798260	Hela-S3	cervix:	n/a	n/a
27	EP300	chr21:17792447-17792711	SK-N-SH_RA	brain:	n/a	n/a
28	ESR1	chr21:17800738-17801435	ECC-1	luminal epithelium:	n/a	chr21:17800982-17800999 chr21:17800983-17801000
29	ESR1	chr21:17792410-17792831	ECC-1	luminal epithelium:	n/a	chr21:17792723-17792740
30	ESR1	chr21:17803418-17803879	ECC-1	luminal epithelium:	n/a	n/a
31	ESR1	chr21:17803565-17803786	ECC-1	luminal epithelium:	n/a	n/a
32	ESR1	chr21:17792349-17792958	ECC-1	luminal epithelium:	n/a	chr21:17792723-17792740
33	ESR1	chr21:17800643-17801437	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	chr21:17800724-17801392	ECC-1	luminal epithelium:	n/a	chr21:17800982-17800999 chr21:17800983-17801000
36	ESR1	chr21:17803443-17803867	ECC-1	luminal epithelium:	n/a	n/a
37	ESR1	chr21:17792414-17792864	ECC-1	luminal epithelium:	n/a	chr21:17792723-17792740
38	ESR1	chr21:17800843-17801192	ECC-1	luminal epithelium:	n/a	chr21:17800982-17800999 chr21:17800983-17801000
39	ESR1	chr21:17803396-17803834	ECC-1	luminal epithelium:	n/a	n/a
40	FOS	chr21:17818346-17818656	MCF10A-Er-Src	breast:	n/a	n/a
41	FOS	chr21:17798165-17798330	MCF10A-Er-Src	breast:	n/a	n/a
42	FOS	chr21:17818346-17818635	MCF10A-Er-Src	breast:	n/a	n/a
43	FOS	chr21:17818869-17819045	MCF10A-Er-Src	breast:	n/a	n/a
44	FOS	chr21:17796729-17797285	HUVEC	blood vessel:	n/a	chr21:17797059-17797069
45	FOS	chr21:17798152-17798305	MCF10A-Er-Src	breast:	n/a	n/a
46	FOS	chr21:17818346-17818632	MCF10A-Er-Src	breast:	n/a	n/a
47	FOS	chr21:17818869-17819102	MCF10A-Er-Src	breast:	n/a	n/a
48	FOS	chr21:17797602-17798217	HUVEC	blood vessel:	n/a	n/a
49	FOXA1	chr21:17791426-17791756	T-47D	breast:	n/a	chr21:17791447-17791459
50	FOXA1	chr21:17792466-17792727	HepG2	liver:	n/a	n/a

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

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

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

Extended variants
information (count: 1633 )
Associated
traits (count: 72 )

Variant overlapped rSNPs/rCNVs (count:1633 , 50 per page) page: 1 2 3 4 5 6 7 ... 33

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs8129788	chr21:17786219-17786220	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs563185984	chr21:17786238-17786239	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs531642293	chr21:17786336-17786337	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs551334404	chr21:17786349-17786350	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs184603725	chr21:17786352-17786353	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs528369221	chr21:17786434-17786435	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs2896758	chr21:17786439-17786440	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
8	rs558416319	chr21:17786468-17786469	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs545251588	chr21:17786479-17786480	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs567398817	chr21:17786515-17786516	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs536440875	chr21:17786522-17786523	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs11909827	chr21:17786530-17786531	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs568383665	chr21:17786578-17786579	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs147015868	chr21:17786616-17786617	Weak transcription Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
15	rs558552029	chr21:17786630-17786631	Weak transcription Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
16	rs73179807	chr21:17786649-17786650	Weak transcription Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
17	rs541077984	chr21:17786669-17786670	Weak transcription Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
18	rs141622546	chr21:17786702-17786703	Weak transcription Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
19	rs112449845	chr21:17786769-17786770	Weak transcription Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
20	rs190321093	chr21:17786772-17786773	Weak transcription Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
21	rs563062606	chr21:17786849-17786850	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs78817900	chr21:17786893-17786894	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs181476904	chr21:17786926-17786927	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs564890421	chr21:17786940-17786941	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs2122251	chr21:17786946-17786947	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
26	rs186295015	chr21:17786959-17786960	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs1449518	chr21:17786964-17786965	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
28	rs529878319	chr21:17786988-17786989	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs141684965	chr21:17787053-17787054	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs539076693	chr21:17787064-17787065	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs376023739	chr21:17787078-17787079	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs552203287	chr21:17787103-17787104	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs572778904	chr21:17787230-17787231	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
34	rs565726371	chr21:17787261-17787262	Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
35	rs534591125	chr21:17787291-17787292	Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
36	rs554400267	chr21:17787310-17787311	Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
37	rs571232112	chr21:17787325-17787326	Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
38	rs34437754	chr21:17787326-17787327	Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
39	rs398036119	chr21:17787336-17787337	Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
40	rs77278993	chr21:17787337-17787338	Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
41	rs536462587	chr21:17787339-17787340	Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
42	rs189287422	chr21:17787359-17787360	Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
43	rs576331398	chr21:17787361-17787362	Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
44	rs9980917	chr21:17787378-17787379	Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
45	rs75670073	chr21:17787388-17787389	Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
46	rs565231716	chr21:17787389-17787390	Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
47	rs572144689	chr21:17787487-17787488	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
48	rs28421726	chr21:17787507-17787508	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
49	rs56178309	chr21:17787514-17787515	Weak transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
50	rs143021577	chr21:17787520-17787521	Weak transcription	Chromatin interactive region	2 gene(s)	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:494 , 50 per page) page: 1 2 3 4 5 6 7 ... 10

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:17771400-17791200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr21:17775400-17786600	Weak transcription	Ovary	ovary
3	chr21:17781000-17789600	Weak transcription	Liver	Liver
4	chr21:17781200-17790400	Weak transcription	NH-A	brain
5	chr21:17786000-17786800	Enhancers	Brain Anterior Caudate	brain
6	chr21:17786200-17788200	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr21:17786600-17786800	Active TSS	Ovary	ovary
8	chr21:17786800-17788200	Weak transcription	Ovary	ovary
9	chr21:17786800-17789200	Weak transcription	Brain Anterior Caudate	brain
10	chr21:17788200-17788400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
11	chr21:17788200-17788400	Enhancers	Right Atrium	heart
12	chr21:17788200-17788600	Enhancers	Brain Angular Gyrus	brain
13	chr21:17788200-17788600	Enhancers	Brain Inferior Temporal Lobe	brain
14	chr21:17788200-17788800	Enhancers	Ovary	ovary
15	chr21:17788400-17790600	Weak transcription	Right Atrium	heart
16	chr21:17788400-17790800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr21:17788600-17790400	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr21:17788600-17790600	Weak transcription	Brain Angular Gyrus	brain
19	chr21:17788800-17791000	Weak transcription	Ovary	ovary
20	chr21:17789200-17789400	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr21:17789200-17789400	Enhancers	Brain Anterior Caudate	brain
22	chr21:17789400-17789600	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr21:17789400-17790000	Weak transcription	Brain Anterior Caudate	brain
24	chr21:17789400-17790000	Enhancers	Brain Germinal Matrix	brain
25	chr21:17789400-17791200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr21:17789600-17789800	Enhancers	Liver	Liver
27	chr21:17789600-17789800	Enhancers	Brain Cingulate Gyrus	brain
28	chr21:17789600-17790400	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr21:17789600-17791000	Enhancers	Fetal Brain Male	brain
30	chr21:17789600-17791400	Enhancers	Brain Hippocampus Middle	brain
31	chr21:17789800-17790200	Weak transcription	Liver	Liver
32	chr21:17789800-17790800	Weak transcription	Brain Cingulate Gyrus	brain
33	chr21:17790000-17790200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr21:17790000-17790400	Weak transcription	Brain Germinal Matrix	brain
35	chr21:17790000-17790600	Enhancers	Brain Anterior Caudate	brain
36	chr21:17790000-17791400	Enhancers	Brain Substantia Nigra	brain
37	chr21:17790200-17790400	Enhancers	Osteobl	bone
38	chr21:17790200-17790800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr21:17790200-17791400	Enhancers	Liver	Liver
40	chr21:17790400-17790600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr21:17790400-17790600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr21:17790400-17790600	Active TSS	Fetal Heart	heart
43	chr21:17790400-17790800	Active TSS	Brain Inferior Temporal Lobe	brain
44	chr21:17790400-17790800	Active TSS	Skeletal Muscle Male	skeletal muscle
45	chr21:17790400-17790800	Active TSS	HSMMtube	muscle
46	chr21:17790400-17790800	Active TSS	NH-A	brain
47	chr21:17790400-17791000	Enhancers	Brain Germinal Matrix	brain
48	chr21:17790400-17791400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr21:17790400-17791400	Enhancers	HUVEC	blood vessel
50	chr21:17790400-17791600	Enhancers	Cortex derived primary cultured neurospheres	brain

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