Variant report

Variant	nsv1003707
Chromosome Location	chr4:19898883-19963213
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLIT2-1	chr4:19910835-19911315	ENSG00000248515.1

Extended variants
information (count: 703 )
Associated
traits (count: 61 )

Variant overlapped rSNPs/rCNVs (count:703 , 50 per page) page: 1 2 3 4 5 6 7 ... 15

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs10938777	chr4:19899817-19899818	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs10938778	chr4:19899862-19899863	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
3	rs147311632	chr4:19899876-19899877	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs12498777	chr4:19899942-19899943	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
5	rs573722293	chr4:19899943-19899944	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs141000994	chr4:19899954-19899955	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs531408837	chr4:19899959-19899960	Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs564267491	chr4:19899968-19899969	Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs550112463	chr4:19899974-19899975	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs72603200	chr4:19899985-19899986	Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs35587015	chr4:19899986-19899987	Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs367921513	chr4:19899987-19899988	Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs568959338	chr4:19910849-19910850	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
14	rs536854241	chr4:19910927-19910928	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
15	rs555175564	chr4:19910929-19910930	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
16	rs374710999	chr4:19910971-19910972	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
17	rs75826209	chr4:19910972-19910973	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
18	rs373430667	chr4:19910973-19910974	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
19	rs561805366	chr4:19910974-19910975	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
20	rs75666765	chr4:19910995-19910996	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
21	rs199661096	chr4:19910996-19910997	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
22	rs534465537	chr4:19910997-19910998	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
23	rs143371566	chr4:19911005-19911006	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
24	rs16868857	chr4:19911053-19911054	Inactive region	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
25	rs532284283	chr4:19911060-19911061	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
26	rs537830543	chr4:19911104-19911105	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
27	rs145579686	chr4:19911116-19911117	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
28	rs183640415	chr4:19911134-19911135	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
29	rs542416257	chr4:19911179-19911180	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
30	rs560706065	chr4:19911199-19911200	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
31	rs79012845	chr4:19911205-19911206	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
32	rs572688939	chr4:19911206-19911207	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
33	rs188202628	chr4:19911214-19911215	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
34	rs565009113	chr4:19911216-19911217	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
35	rs200036449	chr4:19911256-19911257	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
36	rs191425504	chr4:19911269-19911270	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
37	rs550274093	chr4:19911285-19911286	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
38	rs182427840	chr4:19911314-19911315	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
39	rs58812947	chr4:19913611-19913612	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
40	rs145953573	chr4:19913625-19913626	Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs73801279	chr4:19913640-19913641	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
42	rs138573445	chr4:19913662-19913663	Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs55688785	chr4:19913672-19913673	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
44	rs573889575	chr4:19913741-19913742	Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs541411404	chr4:19913753-19913754	Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs111781320	chr4:19913781-19913782	Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs141675136	chr4:19913782-19913783	Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs150762732	chr4:19913801-19913802	Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs563795568	chr4:19913837-19913838	Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs6848057	chr4:19913869-19913870	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a

Variant related diseases (count:61)

Disease	PMID	Source
Oral squamous cell carcinoma	17134496	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Wilms tumour	21544195	CNVD
Breast cancer	17603634	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Colorectal cancer	19359472	CNVD
Neuroblastoma	17533364	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Cancer	21637783	CNVD
Melanoma	21693616	CNVD
Squamous cell cancer	21044232	CNVD
Colorectal cancer	20709793	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Non-small cell lung cancer	21044232	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	17387387	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Cervical cancer	21062161	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Glioblastoma multiforme	21080181	CNVD
Chordoma	21602918	CNVD
HIV/AIDS	22032296	CNVD
Neuroblastoma	18923191	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Breast cancer	21785460	CNVD
Chronic lymphocytic leukemia	20421269	CNVD
Lung cancer	18438408	CNVD
Breast cancer	21858162	CNVD
small cell lung cancer	20016488	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Cancer	21183584	CNVD
Small bowel adenocarcinoma	21586687	CNVD
Gastric cancer	21586687	CNVD
Breast cancer	17133270	CNVD
lymphocytic leukemia	21291569	CNVD
Breast cancer	16608533	CNVD
Non-small cell lung cancer	21829676	CNVD
Melanoma	22183965	CNVD
Multiple myeloma	17550852	CNVD
Prostate cancer	18632612	CNVD
Ovarian cancer	17908972	CNVD
Olfactory neuroblastoma	18408657	CNVD
Burkitt''s lymphoma	20823134	CNVD
Burkitt''s lymphoma	19759907	CNVD
Myelofibrosis	22110671	CNVD
Cancer	20164919	CNVD
Colorectal cancer	16774939	CNVD
Melanoma	20877625	CNVD
Breast cancer	22522925	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:19899800-19900000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:19913600-19914400	Enhancers	Fetal Brain Male	brain
3	chr4:19914400-19916200	Weak transcription	Fetal Brain Male	brain
4	chr4:19916200-19917000	Enhancers	Fetal Brain Male	brain
5	chr4:19916600-19917000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr4:19921800-19922000	Enhancers	Gastric	stomach
7	chr4:19921800-19922200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
8	chr4:19926200-19926800	Enhancers	Dnd41	blood
9	chr4:19929200-19930000	Enhancers	Osteobl	bone
10	chr4:19929200-19930200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr4:19937600-19939000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr4:19937600-19939000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr4:19938000-19938400	Enhancers	Dnd41	blood
14	chr4:19938000-19938600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr4:19938000-19938600	Enhancers	Muscle Satellite Cultured Cells	--
16	chr4:19943000-19943400	Enhancers	NHDF-Ad	bronchial
17	chr4:19943400-19946000	Weak transcription	NHDF-Ad	bronchial
18	chr4:19944800-19948800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr4:19945400-19946200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr4:19945600-19947200	Enhancers	Osteobl	bone
21	chr4:19945800-19946600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr4:19945800-19947400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr4:19945800-19947400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr4:19945800-19947600	Enhancers	HUES64 Cell Line	embryonic stem cell
25	chr4:19946000-19946200	Enhancers	H9 Cell Line	embryonic stem cell
26	chr4:19946000-19947200	Enhancers	NHDF-Ad	bronchial
27	chr4:19946000-19947400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr4:19946000-19947800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr4:19946000-19947800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr4:19946000-19948400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr4:19946000-19948800	Enhancers	HMEC	breast
32	chr4:19946200-19946600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr4:19946200-19947200	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr4:19946200-19947800	Enhancers	HUES6 Cell Line	embryonic stem cell
35	chr4:19946400-19946600	Enhancers	Fetal Lung	lung
36	chr4:19946400-19947400	Enhancers	HUES48 Cell Line	embryonic stem cell
37	chr4:19946400-19947800	Enhancers	H1 Cell Line	embryonic stem cell
38	chr4:19946400-19947800	Enhancers	iPS-18 Cell Line	embryonic stem cell
39	chr4:19946400-19948000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr4:19946400-19949800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr4:19946600-19946800	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr4:19946600-19946800	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
43	chr4:19946600-19947200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr4:19946600-19947400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr4:19946600-19947600	Enhancers	iPS-20b Cell Line	embryonic stem cell
46	chr4:19946600-19947800	Enhancers	Spleen	Spleen
47	chr4:19946600-19949000	Enhancers	HUVEC	blood vessel
48	chr4:19946600-19949800	Enhancers	NHLF	lung
49	chr4:19946800-19947600	Weak transcription	Fetal Lung	lung
50	chr4:19946800-19949600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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