Variant report

Variant	nsv997579
Chromosome Location	chr3:66011-87967
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:6)
LncRNA
region (count:3)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:84119..86199-chr3:87586..89599,2	K562	blood:
2	chr3:84468..85168-chr3:395782..396503,2	MCF-7	breast:
3	chr3:84119..86199-chr3:87586..89599,2	K562	blood:
4	chr3:86365..87356-chr3:395941..396726,2	MCF-7	breast:
5	chr3:84540..85233-chr3:395143..396665,5	MCF-7	breast:
6	chr3:84682..85249-chr3:418773..419384,2	MCF-7	breast:

(count:3 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CHL1-2	chr3:65642-66175	XLOC_002562
2	lnc-CHL1-4	chr3:86531-87048	l_2300_chr3:84309-87048_testes
3	lnc-CHL1-4	chr3:84310-84695	l_2300_chr3:84309-87048_testes

No data

Extended variants
information (count: 298 )
Associated
traits (count: 77 )

Variant overlapped rSNPs/rCNVs (count:298 , 50 per page) page: 1 2 3 4 5 6

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs541078741	chr3:66014-66015	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
2	rs149311860	chr3:66049-66050	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
3	rs535792839	chr3:66074-66075	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
4	rs557283565	chr3:66078-66079	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
5	rs9713920	chr3:66083-66084	Inactive region	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
6	rs539211631	chr3:66107-66108	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
7	rs574859468	chr3:66143-66144	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
8	rs112617705	chr3:66160-66161	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
9	rs35007339	chr3:66164-66165	Inactive region	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
10	rs545839864	chr3:74419-74420	Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs564053938	chr3:74436-74437	Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs528434641	chr3:74460-74461	Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs527773328	chr3:74463-74464	Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs568172730	chr3:74503-74504	Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs112795193	chr3:74506-74507	Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs187780632	chr3:74513-74514	Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs144312387	chr3:74518-74519	Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs537134807	chr3:74523-74524	Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs11128710	chr3:74573-74574	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
20	rs570508914	chr3:74625-74626	Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs534988229	chr3:74628-74629	Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs553590658	chr3:74634-74635	Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs191644857	chr3:74655-74656	Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs369099588	chr3:74666-74667	Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs542378162	chr3:74682-74683	Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs557247718	chr3:74707-74708	Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs11128717	chr3:74710-74711	Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs140133456	chr3:74723-74724	Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs143682940	chr3:74725-74726	Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs73813990	chr3:74734-74735	Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs540175665	chr3:74747-74748	Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs9713456	chr3:74748-74749	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
33	rs146345700	chr3:74767-74768	Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs184112616	chr3:74790-74791	Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs188858453	chr3:75220-75221	Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs532921112	chr3:75229-75230	Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs147604496	chr3:75244-75245	Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs564213103	chr3:75266-75267	Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs73093442	chr3:75276-75277	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
40	rs75301107	chr3:75288-75289	Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs181610241	chr3:75290-75291	Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs185398643	chr3:75306-75307	Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs573853076	chr3:75307-75308	Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs190643164	chr3:75325-75326	Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs551257113	chr3:75332-75333	Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs13326968	chr3:75351-75352	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
47	rs540013875	chr3:75358-75359	Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs13066179	chr3:75375-75376	Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs142209918	chr3:75380-75381	Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs116969138	chr3:75387-75388	Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:77)

Disease	PMID	Source
Cancer	20164920	CNVD
Lung cancer	16618734	CNVD
Autism	18349135	CNVD
Breast cancer	20409316	CNVD
Myelofibrosis	22110671	CNVD
Autism	22241247	CNVD
Intellectual disability	22045946	CNVD
Squamous cell cancer	19607727	CNVD
Gastric adenocarcinoma	19115996	CNVD
sporadic birth defects	19047251	CNVD
Mental retardation	17124404	CNVD
abnormal development	18461090	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Sudden cardiac death	19188705	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Ovarian cancer	21720365	CNVD
Neuroblastoma	18923191	CNVD
Papillary thyroid carcinoma	21436994	CNVD
Biliary cancer	19435499	CNVD
Medulloblastoma	21979893	CNVD
Esophageal squamous carcinoma	18405350	CNVD
Breast cancer	17603634	CNVD
Neuroblastoma	17327916	CNVD
Glioblastoma multiforme	21080181	CNVD
Colorectal cancer	21297112	CNVD
Lynch syndrome	18415027	CNVD
Renal cell carcinoma	18592004	CNVD
Acute myeloid leukemia	20729466	CNVD
Urothelial carcinoma	18382360	CNVD
Melanoma	18172304	CNVD
Cervical cancer	21062161	CNVD
Hirschsprung''s Disease	21712996	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Insulin resistance	16721378	CNVD
Neuroblastoma	18664255	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Multiple myeloma	17077331	CNVD
Ewing''s sarcoma	21437220	CNVD
Neuroblastoma	21484798	CNVD
Non-small cell lung cancer	21044232	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Oral cancer	19627613	CNVD
Renal cell carcinoma	19461508	CNVD
Epithelial cancer	22065749	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Acute myeloid leukemia	16864856	CNVD
Liposarcoma	21253554	CNVD
Basal cell lymphoma	21115979	CNVD
Endometrial cancer	22040021	CNVD
Pancreatic endocrine tumor	20981439	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	17387387	CNVD
Oral cancer	21386901	CNVD
Cutaneous squamous cell carcinomas	19131950	CNVD
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Retinoblastoma	21504564	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
small cell lung cancer	20016488	CNVD
Breast cancer	21364760	CNVD
Schizophrenia	20967226	CNVD
Autism	22543975	CNVD
Attention deficit hyperactivity disorder	19546859	CNVD
Ependymoma	20639864	CNVD
lymphocytic leukemia	21291569	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
Non-syndromic sensorineural hearing loss	17289997	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Renal cell carcinoma	21668985	CNVD
Tetralogy of Fallot	22912587	CNVD
early-passage human iPS cells	21368824	CNVD

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:74400-74800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
2	chr3:75200-75800	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr3:84000-84400	Enhancers	Fetal Brain Male	brain
4	chr3:84200-84600	Enhancers	Fetal Brain Female	brain
5	chr3:84400-85400	Weak transcription	Fetal Brain Male	brain
6	chr3:84800-85200	Enhancers	Brain Germinal Matrix	brain
7	chr3:84800-85200	Active TSS	Fetal Brain Female	brain
8	chr3:84800-85400	Enhancers	Liver	Liver
9	chr3:85200-85800	Enhancers	Fetal Brain Female	brain
10	chr3:85200-85800	Enhancers	HepG2	liver
11	chr3:85400-86000	Flanking Active TSS	Liver	Liver
12	chr3:85400-86200	Enhancers	Fetal Brain Male	brain
13	chr3:85600-85800	Flanking Active TSS	Gastric	stomach
14	chr3:85600-86000	Bivalent Enhancer	Fetal Kidney	kidney
15	chr3:85800-86000	ZNF genes & repeats	Gastric	stomach
16	chr3:85800-86200	Flanking Active TSS	HepG2	liver
17	chr3:86000-86800	Enhancers	Liver	Liver
18	chr3:86200-86800	Enhancers	HepG2	liver
19	chr3:86800-87800	Weak transcription	HepG2	liver

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