Variant report

Variant	nsv1006533
Chromosome Location	chr2:10030964-10065624
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:52)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:52 , 50 per page) page: 1 2

No.	Distal block	Cell Line	Cell type
1	chr2:10033449..10037613-chr2:10038043..10042119,5	MCF-7	breast:
2	chr2:10049796..10051308-chr2:10053649..10056131,2	K562	blood:
3	chr2:10054070..10056636-chr2:10061535..10064977,4	MCF-7	breast:
4	chr2:10055984..10058361-chr2:10061943..10063449,2	MCF-7	breast:
5	chr2:9985747..9988019-chr2:10062440..10064881,2	MCF-7	breast:
6	chr2:10037000..10039031-chr2:10044234..10045895,2	MCF-7	breast:
7	chr2:10047372..10050689-chr2:10052531..10055799,4	MCF-7	breast:
8	chr2:10045085..10047212-chr2:10048163..10049823,2	K562	blood:
9	chr2:10032485..10035098-chr2:10036586..10038853,2	K562	blood:
10	chr2:10047372..10050689-chr2:10052531..10055799,4	MCF-7	breast:
11	chr2:10035308..10037799-chr2:10038582..10040182,2	MCF-7	breast:
12	chr2:10053405..10055914-chr2:10061703..10065567,3	K562	blood:
13	chr2:10045831..10047655-chr2:10091725..10093739,2	MCF-7	breast:
14	chr2:10037000..10039031-chr2:10044234..10045895,2	MCF-7	breast:
15	chr2:10037952..10040907-chr2:10047681..10050214,2	K562	blood:
16	chr2:10049796..10051308-chr2:10053649..10056131,2	K562	blood:
17	chr2:10037949..10040040-chr2:10055239..10057291,2	MCF-7	breast:
18	chr2:10054861..10056659-chr2:10057768..10060141,2	K562	blood:
19	chr2:9982829..9984877-chr2:10036163..10037908,3	MCF-7	breast:
20	chr2:10058951..10060878-chr2:10081099..10082615,2	K562	blood:
21	chr2:10027283..10029259-chr2:10030456..10033188,2	K562	blood:
22	chr2:10053405..10055914-chr2:10061703..10065567,3	K562	blood:
23	chr2:9982531..9984237-chr2:10032924..10035073,2	MCF-7	breast:
24	chr2:9983243..9984795-chr2:10042473..10044081,2	K562	blood:
25	chr2:10035308..10037799-chr2:10038582..10040182,2	MCF-7	breast:
26	chr2:10023869..10026802-chr2:10030630..10033505,2	K562	blood:
27	chr2:10037952..10040907-chr2:10047681..10050214,2	K562	blood:
28	chr2:10033449..10037613-chr2:10038043..10042119,5	MCF-7	breast:
29	chr2:10022528..10025369-chr2:10031502..10033505,2	K562	blood:
30	chr2:10053405..10055914-chr2:10061703..10064557,2	K562	blood:
31	chr2:10036313..10038528-chr2:10044301..10045845,2	MCF-7	breast:
32	chr2:10053405..10055914-chr2:10061703..10064557,2	K562	blood:
33	chr2:10054070..10056636-chr2:10061535..10064977,4	MCF-7	breast:
34	chr2:10036109..10038742-chr2:10044743..10047677,2	K562	blood:
35	chr2:10055984..10058361-chr2:10061943..10063449,2	MCF-7	breast:
36	chr2:10040912..10043798-chr2:10089997..10091829,3	MCF-7	breast:
37	chr2:9940167..9943661-chr2:10053697..10057580,3	MCF-7	breast:
38	chr2:10028962..10031960-chr2:10261510..10264427,2	K562	blood:
39	chr2:10054861..10056659-chr2:10057768..10060141,2	K562	blood:
40	chr2:10039201..10042198-chr2:10045779..10048080,2	MCF-7	breast:
41	chr2:10037949..10040040-chr2:10055239..10057291,2	MCF-7	breast:
42	chr2:10036109..10038742-chr2:10044743..10047677,2	K562	blood:
43	chr2:9940189..9942989-chr2:10049056..10050927,2	MCF-7	breast:
44	chr2:10045993..10047524-chr2:10050988..10053341,2	K562	blood:
45	chr2:10039201..10042198-chr2:10045779..10048080,2	MCF-7	breast:
46	chr2:10045085..10047212-chr2:10048163..10049823,2	K562	blood:
47	chr2:10025374..10028699-chr2:10030128..10032449,3	MCF-7	breast:
48	chr2:9948070..9949733-chr2:10038866..10041132,2	K562	blood:
49	chr2:10032485..10035098-chr2:10036586..10038853,2	K562	blood:
50	chr2:10045993..10047524-chr2:10050988..10053341,2	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CYS1-8	chr2:10062861-10063502	l_1772_chr2:10062860-10067461_breast

No data

Variant related genes	Relation type
ENSG00000171848	chromatin interactions
ENSG00000115750	chromatin interactions
ENSG00000134317	chromatin interactions

Extended variants
information (count: 1341 )
Associated
traits (count: 64 )

Variant overlapped rSNPs/rCNVs (count:1341 , 50 per page) page: 1 2 3 4 5 6 7 ... 27

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs4669481	chr2:10030964-10030965	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs568704440	chr2:10030965-10030966	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs180797256	chr2:10030968-10030969	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
4	rs561885444	chr2:10031003-10031004	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs372923121	chr2:10031036-10031037	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
6	rs56382546	chr2:10031047-10031048	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
7	rs386643059	chr2:10031056-10031057	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs67544747	chr2:10031057-10031058	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs548734455	chr2:10031063-10031064	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs56102002	chr2:10031089-10031090	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
11	rs556041212	chr2:10031121-10031122	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs56258032	chr2:10031129-10031130	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
13	rs112893290	chr2:10031161-10031162	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	mRNA abundance
14	rs571469575	chr2:10031188-10031189	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs557937352	chr2:10031205-10031206	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs577987796	chr2:10031215-10031216	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs540219282	chr2:10031217-10031218	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs560027893	chr2:10031232-10031233	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs149336446	chr2:10031261-10031262	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs537252943	chr2:10031278-10031279	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs403303	chr2:10031389-10031390	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
22	rs403317	chr2:10031404-10031405	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
23	rs4669484	chr2:10031445-10031446	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
24	rs367734003	chr2:10031476-10031477	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
25	rs377710393	chr2:10031509-10031510	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs527290162	chr2:10031515-10031516	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs147454728	chr2:10031586-10031587	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
28	rs6722572	chr2:10031637-10031638	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
29	rs371175159	chr2:10031653-10031654	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
30	rs536184288	chr2:10031713-10031714	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
31	rs549684510	chr2:10031723-10031724	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs376037609	chr2:10031725-10031726	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
33	rs185682045	chr2:10031742-10031743	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs454269	chr2:10031743-10031744	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
35	rs6707700	chr2:10031756-10031757	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
36	rs578005486	chr2:10031764-10031765	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs555226293	chr2:10031812-10031813	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
38	rs553798243	chr2:10031819-10031820	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
39	rs573679928	chr2:10031837-10031838	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
40	rs542526566	chr2:10031841-10031842	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs114219738	chr2:10031874-10031875	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
42	rs35300373	chr2:10031912-10031913	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
43	rs539093420	chr2:10032030-10032031	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs544835020	chr2:10032036-10032037	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs448287	chr2:10032041-10032042	Weak transcription Strong transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
46	rs529330072	chr2:10032097-10032098	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs143856510	chr2:10032156-10032157	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs190690996	chr2:10032253-10032254	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
49	rs450643	chr2:10032297-10032298	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
50	rs549721372	chr2:10032326-10032327	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:64)

Disease	PMID	Source
Breast cancer	17133270	CNVD
Mental retardation	17847001	CNVD
Glioblastoma multiforme	21080181	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Cancer	20164920	CNVD
Neuroblastoma	21508638	CNVD
Breast cancer	17603634	CNVD
Cancer	16751803	CNVD
Neuroblastoma	16790693	CNVD
Colorectal cancer	16272173	CNVD
Breast cancer	17393978	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Medulloblastoma	21979893	CNVD
Lynch syndrome	18415027	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Ovarian neoplasms	16753589	CNVD
Glioblastoma multiforme	17387387	CNVD
Neuroblastoma	17533364	CNVD
Neuroblastoma	18923191	CNVD
Endometrial cancer	22040021	CNVD
Adrenal tumor	17535989	CNVD
Breast cancer	21264507	CNVD
Basal cell lymphoma	17053054	CNVD
Medulloblastoma	17522785	CNVD
Cancer	23418310	CNVD
Ewing''s sarcoma	21437220	CNVD
Ependymoma	16718352	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	18458336	CNVD
lymphocytic leukemia	21291569	CNVD
Prostate cancer	18632612	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Bladder cancer	21909424	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Cancer	20164919	CNVD
Hodgkin''s lymphoma	18641027	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Breast cancer	21364760	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Follicular lymphoma	20505157	CNVD
Autism	17483303	CNVD
Breast cancer	21804112	CNVD
Myelofibrosis	22110671	CNVD
Glioblastoma multiforme	22286061	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
Glioma	17123091	CNVD
Breast cancer	20409316	CNVD
Multiple myeloma	16616336	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Neuroblastoma	18923524	CNVD
Esophageal adenocarcinoma	18519675	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD
early-passage human iPS cells	21368824	CNVD
Ependymoma	18628472	CNVD
Leukemia	18628472	CNVD

Chromatin state (count:1028 , 50 per page) page: 1 2 3 4 5 6 7 ... 21

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:9987200-10038400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr2:9993800-10079600	Weak transcription	Gastric	stomach
3	chr2:9995800-10038000	Weak transcription	Small Intestine	intestine
4	chr2:9998200-10035600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr2:9998800-10032200	Weak transcription	Fetal Heart	heart
6	chr2:9998800-10036400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr2:9999000-10035800	Weak transcription	Brain Hippocampus Middle	brain
8	chr2:9999000-10035800	Weak transcription	Brain Substantia Nigra	brain
9	chr2:9999000-10037000	Weak transcription	Brain Cingulate Gyrus	brain
10	chr2:9999000-10037200	Weak transcription	Colon Smooth Muscle	Colon
11	chr2:9999200-10036200	Weak transcription	Brain Angular Gyrus	brain
12	chr2:9999200-10036400	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr2:9999200-10053800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr2:10014800-10045400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr2:10015000-10036200	Weak transcription	Fetal Kidney	kidney
16	chr2:10017600-10036200	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr2:10017800-10073000	Weak transcription	Right Ventricle	heart
18	chr2:10018400-10035600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr2:10018800-10036200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr2:10019000-10036000	Weak transcription	Stomach Mucosa	stomach
21	chr2:10019800-10037200	Weak transcription	HUVEC	blood vessel
22	chr2:10020200-10032200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr2:10020400-10037400	Weak transcription	K562	blood
24	chr2:10023800-10035000	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr2:10023800-10035800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr2:10024400-10034800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr2:10024400-10036000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr2:10024400-10037600	Weak transcription	Psoas Muscle	Psoas
29	chr2:10024400-10053800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr2:10024600-10036400	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr2:10024600-10037600	Weak transcription	Pancreas	Pancrea
32	chr2:10024800-10036200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr2:10024800-10036400	Weak transcription	Rectal Smooth Muscle	rectum
34	chr2:10024800-10047600	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr2:10024800-10051400	Weak transcription	Duodenum Mucosa	Duodenum
36	chr2:10025000-10031600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr2:10025000-10032200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr2:10025000-10036200	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr2:10025000-10047000	Weak transcription	Thymus	Thymus
40	chr2:10025000-10053800	Weak transcription	Fetal Muscle Trunk	muscle
41	chr2:10025000-10053800	Weak transcription	Ovary	ovary
42	chr2:10025000-10054400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr2:10025000-10054400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr2:10025000-10054400	Weak transcription	Spleen	Spleen
45	chr2:10025200-10035400	Weak transcription	Fetal Thymus	thymus
46	chr2:10025200-10035800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr2:10025400-10052600	Weak transcription	Left Ventricle	heart
48	chr2:10025800-10035000	Weak transcription	HMEC	breast
49	chr2:10025800-10036600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr2:10026000-10032200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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