Variant report

Variant	nsv523900
Chromosome Location	chr21:40506026-40509189
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:40105479..40106305-chr21:40507907..40508515,2	MCF-7	breast:
2	chr21:40177357..40179750-chr21:40506516..40509487,2	MCF-7	breast:
3	chr21:40040912..40041817-chr21:40507070..40508725,4	MCF-7	breast:
4	chr21:40277363..40279174-chr21:40508328..40510405,2	K562	blood:
5	chr21:40508919..40510816-chr21:40719509..40722111,2	K562	blood:

Variant related genes	Relation type
ENSG00000157557	chromatin interactions
ENSG00000205581	chromatin interactions

Extended variants
information (count: 123 )
Associated
traits (count: 72 )

Variant overlapped rSNPs/rCNVs (count:123 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs4816612	chr21:40506026-40506027	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs138632401	chr21:40506038-40506039	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs142715731	chr21:40506045-40506046	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs2836911	chr21:40506049-40506050	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
5	rs4817991	chr21:40506060-40506061	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
6	rs563551517	chr21:40506110-40506111	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs532512955	chr21:40506123-40506124	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs544980734	chr21:40506188-40506189	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs2836912	chr21:40506194-40506195	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
10	rs527573051	chr21:40506203-40506204	Weak transcription Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
11	rs547658353	chr21:40506226-40506227	Weak transcription Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
12	rs144373516	chr21:40506257-40506258	Weak transcription Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
13	rs148383169	chr21:40506260-40506261	Weak transcription Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
14	rs549813764	chr21:40506301-40506302	Weak transcription Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
15	rs569572680	chr21:40506337-40506338	Weak transcription Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
16	rs141497649	chr21:40506377-40506378	Weak transcription Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
17	rs558995535	chr21:40506389-40506390	Weak transcription Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
18	rs566080023	chr21:40506404-40506405	Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
19	rs373753073	chr21:40506469-40506470	Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
20	rs534965773	chr21:40506484-40506485	Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
21	rs111420186	chr21:40506491-40506492	Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
22	rs542884869	chr21:40506518-40506519	Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs7278600	chr21:40506531-40506532	Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
24	rs7278231	chr21:40506532-40506533	Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
25	rs555621953	chr21:40506540-40506541	Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs373490522	chr21:40506548-40506549	Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs532696454	chr21:40506561-40506562	Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
28	rs541220450	chr21:40506597-40506598	Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs2142113	chr21:40506615-40506616	Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
30	rs200027524	chr21:40506642-40506643	Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
31	rs562970303	chr21:40506654-40506655	Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs2142114	chr21:40506661-40506662	Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
33	rs536329766	chr21:40506662-40506663	Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs200359093	chr21:40506670-40506671	Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs557382368	chr21:40506685-40506686	Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs577179886	chr21:40506700-40506701	Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs546222012	chr21:40506704-40506705	Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
38	rs559778803	chr21:40506759-40506760	Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
39	rs527610094	chr21:40506767-40506768	Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
40	rs541314150	chr21:40506786-40506787	Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs191037055	chr21:40506788-40506789	Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
42	rs529869348	chr21:40506803-40506804	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
43	rs139380353	chr21:40506822-40506823	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
44	rs113932461	chr21:40506827-40506828	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
45	rs144290930	chr21:40506828-40506829	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
46	rs181504532	chr21:40506850-40506851	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs367808349	chr21:40506886-40506887	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
48	rs565321348	chr21:40506925-40506926	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
49	rs73217539	chr21:40506929-40506930	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
50	rs186153309	chr21:40506939-40506940	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:72)

Disease	PMID	Source
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
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
Prostate cancer	19156837	CNVD
Basal cell lymphoma	17170743	CNVD
Follicular lymphoma	17170743	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
small cell lung cancer	20016488	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
lymphocytic leukemia	21291569	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
Chronic lymphocytic leukemia	20421269	CNVD
Wilms tumour	21544195	CNVD
Ewing''s sarcoma	17952124	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Breast cancer	21364760	CNVD
Acute myeloid leukemia	16864856	CNVD
Mental retardation	21031080	CNVD
Polymicrogyria	21031080	CNVD
periventricular nodular heterotopia	21031080	CNVD
Myelodysplastic syndrome	21606161	CNVD
Chronic lymphocytic leukemia	18922857	CNVD
Autism	18414403	CNVD
Gastrointestinal stromal cancer	19259404	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Breast cancer	21858162	CNVD
Neuroblastoma	18923191	CNVD
Breast cancer	17899364	CNVD
Down syndrome	20877625	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Cancer	20164920	CNVD
Myelofibrosis	22110671	CNVD
Hirschsprung''s Disease	21712996	CNVD
Prostate cancer	21147910	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Prostate cancer	17245344	CNVD
Prostate cancer	20473283	CNVD
Chordoma	18071362	CNVD
Breast cancer	22522925	CNVD
T-cell lymphomas	22341440	CNVD
Pancreatic cancer	17952125	CNVD
Cancer	20164919	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40497800-40506200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr21:40503400-40508600	Weak transcription	Esophagus	oesophagus
3	chr21:40503600-40506200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr21:40503600-40508400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr21:40503800-40508800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr21:40504000-40508800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr21:40504800-40509400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr21:40505000-40510000	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr21:40505200-40508600	Weak transcription	Placenta	Placenta
10	chr21:40505600-40507200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr21:40505600-40507400	Weak transcription	HepG2	liver
12	chr21:40506200-40506400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr21:40506200-40506400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr21:40506200-40506600	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr21:40506400-40506600	Enhancers	Fetal Kidney	kidney
16	chr21:40506400-40506800	Bivalent/Poised TSS	Fetal Brain Male	brain
17	chr21:40506400-40506800	Bivalent Enhancer	K562	blood
18	chr21:40506400-40507200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr21:40506400-40508600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr21:40506600-40506800	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
21	chr21:40506600-40506800	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr21:40506800-40508600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr21:40506800-40508800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr21:40507200-40509800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr21:40507200-40510200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr21:40507400-40509800	Enhancers	Spleen	Spleen
27	chr21:40507400-40510600	Enhancers	HepG2	liver
28	chr21:40507800-40509000	Weak transcription	Fetal Kidney	kidney
29	chr21:40508000-40508200	Enhancers	Dnd41	blood
30	chr21:40508200-40509200	Weak transcription	Dnd41	blood
31	chr21:40508400-40509400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr21:40508400-40509600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr21:40508400-40509600	Enhancers	NHEK	skin
34	chr21:40508400-40509800	Enhancers	HMEC	breast
35	chr21:40508400-40509800	Enhancers	NHDF-Ad	bronchial
36	chr21:40508600-40508800	Enhancers	Fetal Muscle Trunk	muscle
37	chr21:40508600-40509600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr21:40508600-40509600	Enhancers	Esophagus	oesophagus
39	chr21:40508600-40509600	Enhancers	Placenta	Placenta
40	chr21:40508600-40509600	Enhancers	Osteobl	bone
41	chr21:40508600-40509800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr21:40508600-40509800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr21:40508600-40509800	Enhancers	Fetal Muscle Leg	muscle
44	chr21:40508600-40509800	Enhancers	Placenta Amnion	Placenta Amnion
45	chr21:40508600-40510000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr21:40508600-40510000	Enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr21:40508600-40510000	Enhancers	A549	lung
48	chr21:40508600-40510000	Enhancers	NHLF	lung
49	chr21:40508600-40510400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr21:40508600-40510600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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