Variant report

Variant	nsv589951
Chromosome Location	chr3:24746378-24816974
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:16)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:24814934..24815742-chr3:25136008..25136648,2	MCF-7	breast:
2	chr3:24766490..24768818-chr3:24773482..24775957,2	K562	blood:
3	chr3:24802431..24804243-chr3:24805497..24807982,2	K562	blood:
4	chr3:24815278..24815959-chr3:25635331..25636072,2	MCF-7	breast:
5	chr3:24766490..24768818-chr3:24773482..24775957,2	K562	blood:
6	chr3:24755192..24756974-chr3:24759928..24761810,2	K562	blood:
7	chr3:24814926..24815573-chr3:25074600..25075173,3	MCF-7	breast:
8	chr3:24751127..24751647-chr3:149088018..149088599,2	Hela-S3	cervix:
9	chr3:24755192..24756974-chr3:24759928..24761810,2	K562	blood:
10	chr3:24802431..24804243-chr3:24805497..24807982,2	K562	blood:
11	chr3:24797378..24798887-chr3:24799075..24801022,2	K562	blood:
12	chr3:24745399..24747659-chr3:24751181..24753513,2	K562	blood:
13	chr3:24815127..24815890-chr3:25004964..25005522,2	MCF-7	breast:
14	chr3:24727648..24729843-chr3:24805310..24807941,2	K562	blood:
15	chr3:24797378..24798887-chr3:24799075..24801022,2	K562	blood:
16	chr3:24745399..24747659-chr3:24751181..24753513,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RARB-1	chr3:24803731-24803785	ENSG00000237838

No data

Variant related genes	Relation type
ENSG00000237838	chromatin interactions

Extended variants
information (count: 1647 )
Associated
traits (count: 71 )

Variant overlapped rSNPs/rCNVs (count:1647 , 50 per page) page: 1 2 3 4 5 6 7 ... 33

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs9862855	chr3:24746378-24746379	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs367697391	chr3:24746380-24746381	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs114315209	chr3:24746386-24746387	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs4558693	chr3:24746454-24746455	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
5	rs151283371	chr3:24746471-24746472	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs546505670	chr3:24746476-24746477	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs529532272	chr3:24746495-24746496	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs191977729	chr3:24746537-24746538	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs199523772	chr3:24746567-24746568	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs565880701	chr3:24746575-24746576	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs116054126	chr3:24746585-24746586	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs551820502	chr3:24746629-24746630	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs3934760	chr3:24746641-24746642	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
14	rs533924891	chr3:24746646-24746647	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs184720687	chr3:24746654-24746655	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs567442110	chr3:24746668-24746669	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs189533164	chr3:24746684-24746685	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs201495049	chr3:24746687-24746688	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs555897499	chr3:24746690-24746691	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs116306848	chr3:24746723-24746724	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs544677926	chr3:24746724-24746725	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs139968676	chr3:24746780-24746781	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs73820034	chr3:24746794-24746795	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
24	rs147720684	chr3:24746800-24746801	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs562452396	chr3:24746832-24746833	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs3934758	chr3:24746852-24746853	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
27	rs181540895	chr3:24746881-24746882	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs73048329	chr3:24746886-24746887	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
29	rs73048330	chr3:24746907-24746908	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs150275771	chr3:24746942-24746943	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs3934759	chr3:24746951-24746952	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
32	rs145852552	chr3:24746968-24746969	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs549059118	chr3:24747011-24747012	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs4073046	chr3:24747030-24747031	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
35	rs537716776	chr3:24747044-24747045	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs555963049	chr3:24747063-24747064	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs571139207	chr3:24747064-24747065	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs4073047	chr3:24747066-24747067	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
39	rs112798830	chr3:24747070-24747071	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs529742032	chr3:24747102-24747103	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs572044383	chr3:24747125-24747126	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs184233324	chr3:24747200-24747201	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs574078665	chr3:24747250-24747251	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs199640262	chr3:24747270-24747271	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs201248124	chr3:24747271-24747272	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs574296356	chr3:24747287-24747288	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs563007417	chr3:24747358-24747359	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs544947874	chr3:24747367-24747368	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs578235027	chr3:24747368-24747369	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs4072363	chr3:24747419-24747420	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a

Variant related diseases (count:71)

Disease	PMID	Source
Esophageal squamous carcinoma	18405350	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Breast cancer	17603634	CNVD
Neuroblastoma	17327916	CNVD
Glioblastoma multiforme	21080181	CNVD
Neuroblastoma	18923191	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
Oral squamous cell carcinoma	17134496	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
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Retinoblastoma	21504564	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
lymphocytic leukemia	21291569	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Renal cell carcinoma	21668985	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Lung cancer	20668451	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Intellectual disability	22102821	CNVD
Esophageal cancer	20955586	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Squamous cell cancer	20885788	CNVD
Breast cancer	17133270	CNVD
Uveal melanoma	20484589	CNVD
Autism	22495311	CNVD
Melanoma	20688739	CNVD
Myelofibrosis	22110671	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:24745000-24746800	Enhancers	Skeletal Muscle Female	skeletal muscle
2	chr3:24745000-24747000	Enhancers	HMEC	breast
3	chr3:24745200-24746800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:24745200-24747000	Enhancers	NHEK	skin
5	chr3:24745600-24747000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr3:24745600-24747000	Enhancers	A549	lung
7	chr3:24745600-24747000	Enhancers	Hela-S3	cervix
8	chr3:24745600-24747200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr3:24745800-24746800	Enhancers	Muscle Satellite Cultured Cells	--
10	chr3:24745800-24747000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr3:24745800-24754400	Weak transcription	Aorta	Aorta
12	chr3:24746000-24746400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr3:24746000-24746800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr3:24746400-24747000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr3:24746400-24747000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr3:24746400-24749600	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr3:24747600-24747800	Enhancers	Gastric	stomach
18	chr3:24749600-24754800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr3:24751200-24752200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr3:24754200-24756000	Enhancers	Pancreatic Islets	Pancreatic Islet
21	chr3:24754400-24755600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr3:24754400-24756400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr3:24754400-24756400	Enhancers	Aorta	Aorta
24	chr3:24754800-24755800	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr3:24755000-24755400	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr3:24755000-24755600	Enhancers	HUES48 Cell Line	embryonic stem cell
27	chr3:24755000-24755800	Enhancers	Fetal Lung	lung
28	chr3:24755200-24755400	Enhancers	Muscle Satellite Cultured Cells	--
29	chr3:24763600-24763800	Active TSS	Skeletal Muscle Female	skeletal muscle
30	chr3:24763600-24764200	Enhancers	Skeletal Muscle Male	skeletal muscle
31	chr3:24763800-24764000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
32	chr3:24764000-24765000	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr3:24764200-24767000	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr3:24764400-24764600	Enhancers	Psoas Muscle	Psoas
35	chr3:24764600-24767400	Weak transcription	Psoas Muscle	Psoas
36	chr3:24766400-24767200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr3:24766400-24768000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr3:24766400-24768000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr3:24766400-24768200	Enhancers	NHEK	skin
40	chr3:24766600-24768200	Enhancers	HMEC	breast
41	chr3:24767000-24767400	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr3:24767200-24767600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr3:24767200-24768200	Enhancers	Placenta Amnion	Placenta Amnion
44	chr3:24767600-24768200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr3:24768000-24768400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr3:24768000-24775200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr3:24768200-24771200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr3:24768200-24771200	Weak transcription	NHEK	skin
49	chr3:24768200-24771400	Weak transcription	HMEC	breast
50	chr3:24768400-24773200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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