Variant report

Variant	nsv460307
Chromosome Location	chr3:287419-311851
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:291331..293955-chr3:294697..297452,2	MCF-7	breast:
2	chr3:297411..299702-chr3:300779..302869,2	K562	blood:
3	chr3:297411..299702-chr3:300779..302869,2	K562	blood:
4	chr3:291331..293955-chr3:294697..297452,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CNTN6-7	chr3:288251-288539	NONHSAT087560
2	lnc-CNTN6-7	chr3:288251-290282	NONHSAT087561

Extended variants
information (count: 1306 )
Associated
traits (count: 83 )

Variant overlapped rSNPs/rCNVs (count:1306 , 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	rs455357	chr3:287419-287420	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs573933476	chr3:287438-287439	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs562954139	chr3:287449-287450	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs191483548	chr3:287460-287461	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs368243129	chr3:287507-287508	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs183796734	chr3:287571-287572	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs76261264	chr3:287642-287643	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs77473791	chr3:287662-287663	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs561352491	chr3:287774-287775	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs571076911	chr3:287784-287785	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs559849775	chr3:287786-287787	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs535300443	chr3:287797-287798	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs146020496	chr3:287847-287848	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs571356293	chr3:287862-287863	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs76660477	chr3:287876-287877	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs547279055	chr3:287880-287881	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs376831622	chr3:287909-287910	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs565682476	chr3:287967-287968	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs568464218	chr3:287991-287992	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs188630845	chr3:288022-288023	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs192602187	chr3:288030-288031	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs576051620	chr3:288118-288119	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs564342908	chr3:288119-288120	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs183471491	chr3:288172-288173	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs556680617	chr3:288178-288179	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs578104996	chr3:288196-288197	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs186696888	chr3:288219-288220	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs560745957	chr3:288220-288221	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs191452451	chr3:288261-288262	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
30	rs543009125	chr3:288283-288284	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
31	rs561289488	chr3:288336-288337	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
32	rs138779030	chr3:288447-288448	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
33	rs550015930	chr3:288509-288510	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
34	rs565417365	chr3:288529-288530	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
35	rs184752078	chr3:288531-288532	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
36	rs532203662	chr3:288543-288544	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
37	rs547216375	chr3:288557-288558	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
38	rs565621366	chr3:288573-288574	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
39	rs536154334	chr3:288575-288576	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
40	rs371273930	chr3:288612-288613	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
41	rs117018529	chr3:288634-288635	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
42	rs537092845	chr3:288645-288646	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
43	rs141248350	chr3:288655-288656	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
44	rs189957906	chr3:288669-288670	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
45	rs576900803	chr3:288685-288686	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
46	rs539221354	chr3:288756-288757	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
47	rs625589	chr3:288775-288776	Weak transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
48	rs572749996	chr3:288817-288818	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
49	rs543345444	chr3:288858-288859	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
50	rs3901524	chr3:288864-288865	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a

Variant related diseases (count:83)

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
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
Acute lymphoblastic leukemia	20435627	CNVD
Autism	20685689	CNVD
Melanoma	20877625	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD
Multiple myeloma	17550852	CNVD
Prostate cancer	18632612	CNVD
Thoracic aortic aneurysm	21092924	CNVD

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:283200-290800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:285200-290600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr3:285400-289200	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr3:285400-290800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr3:285400-307400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr3:285800-289200	Weak transcription	Fetal Brain Male	brain
7	chr3:286000-289400	Weak transcription	Fetal Lung	lung
8	chr3:286200-288800	Weak transcription	Fetal Brain Female	brain
9	chr3:286200-288800	Weak transcription	Fetal Muscle Leg	muscle
10	chr3:286200-315400	Weak transcription	Ovary	ovary
11	chr3:286600-289400	Weak transcription	Brain Germinal Matrix	brain
12	chr3:286600-290800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr3:287400-287600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr3:288800-289400	Enhancers	Fetal Muscle Leg	muscle
15	chr3:288800-291400	Enhancers	Fetal Brain Female	brain
16	chr3:289200-289800	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr3:289200-289800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
18	chr3:289200-291200	Enhancers	Fetal Brain Male	brain
19	chr3:289400-290800	Weak transcription	Fetal Muscle Leg	muscle
20	chr3:289400-291400	Enhancers	Fetal Lung	lung
21	chr3:289400-291800	Enhancers	Brain Germinal Matrix	brain
22	chr3:289600-291600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr3:289800-296400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr3:290400-291400	Enhancers	Fetal Kidney	kidney
25	chr3:290600-291400	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr3:290600-291600	Enhancers	HepG2	liver
27	chr3:290600-291800	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr3:290600-292800	Enhancers	Primary B cells from peripheral blood	blood
29	chr3:290800-291000	Enhancers	Fetal Muscle Leg	muscle
30	chr3:290800-291200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr3:290800-291200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr3:290800-291400	Enhancers	Pancreatic Islets	Pancreatic Islet
33	chr3:290800-291800	Enhancers	iPS-20b Cell Line	embryonic stem cell
34	chr3:290800-292400	Enhancers	Primary B cells from cord blood	blood
35	chr3:291000-291600	Enhancers	iPS-18 Cell Line	embryonic stem cell
36	chr3:291200-298200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr3:291400-292600	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr3:291400-299600	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr3:291800-296800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr3:291800-305200	Weak transcription	Brain Germinal Matrix	brain
41	chr3:292600-292800	Enhancers	Pancreatic Islets	Pancreatic Islet
42	chr3:296200-296400	Enhancers	ES-I3 Cell Line	embryonic stem cell
43	chr3:296400-296600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
44	chr3:296400-297200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr3:296400-297200	Enhancers	HUES6 Cell Line	embryonic stem cell
46	chr3:296800-297000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
47	chr3:296800-297400	Enhancers	iPS-20b Cell Line	embryonic stem cell
48	chr3:297000-297600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr3:297000-299600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr3:297200-297600	Enhancers	ES-I3 Cell Line	embryonic stem cell

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