Variant report

Variant	nsv965149
Chromosome Location	chr3:24138426-24140099
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BRCA1	chr3:24139823-24139826	GM12878	blood:	n/a	n/a
2	CTCF	chr3:24139288-24139407	GM20000	blood:	n/a	n/a
3	SPI1	chr3:24139597-24139735	K562	blood:	n/a	n/a
4	STAT3	chr3:24140045-24140245	MCF10A-Er-Src	breast:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-THRB-1	chr3:24137760-24138924	ENSG00000224074.2
2	lnc-THRB-1	chr3:24137780-24138924	NONHSAT088693

Variant related genes	Relation type
NPM1P23	TF binding region

Extended variants
information (count: 97 )
Associated
traits (count: 71 )

Variant overlapped rSNPs/rCNVs (count:97 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs533124687	chr3:24138447-24138448	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
2	rs537172191	chr3:24138487-24138488	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
3	rs183904085	chr3:24138495-24138496	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
4	rs370181208	chr3:24138520-24138521	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
5	rs113148095	chr3:24138565-24138566	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
6	rs186860497	chr3:24138592-24138593	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
7	rs60523116	chr3:24138650-24138651	Weak transcription Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
8	rs75566695	chr3:24138663-24138664	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
9	rs144101140	chr3:24138673-24138674	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
10	rs572658673	chr3:24138679-24138680	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
11	rs114699947	chr3:24138699-24138700	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
12	rs575146805	chr3:24138706-24138707	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
13	rs545606456	chr3:24138712-24138713	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
14	rs115116685	chr3:24138718-24138719	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
15	rs532645238	chr3:24138719-24138720	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
16	rs368181451	chr3:24138734-24138735	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
17	rs547590209	chr3:24138738-24138739	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
18	rs111907134	chr3:24138743-24138744	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
19	rs559482299	chr3:24138758-24138759	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
20	rs530345481	chr3:24138761-24138762	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
21	rs548445542	chr3:24138762-24138763	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
22	rs569979842	chr3:24138767-24138768	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
23	rs537438995	chr3:24138768-24138769	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
24	rs552432790	chr3:24138786-24138787	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
25	rs72617500	chr3:24138799-24138800	Weak transcription Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
26	rs535071274	chr3:24138800-24138801	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
27	rs553212294	chr3:24138837-24138838	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
28	rs574650642	chr3:24138864-24138865	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
29	rs535767567	chr3:24138874-24138875	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
30	rs190698634	chr3:24138893-24138894	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
31	rs557196872	chr3:24138910-24138911	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
32	rs575164441	chr3:24138933-24138934	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs545773317	chr3:24138938-24138939	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs111993772	chr3:24138941-24138942	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs9839486	chr3:24138988-24138989	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
36	rs572615661	chr3:24139033-24139034	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs539908900	chr3:24139049-24139050	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs559545599	chr3:24139052-24139053	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs146483186	chr3:24139071-24139072	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs542194371	chr3:24139095-24139096	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs535580330	chr3:24139117-24139118	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs141161369	chr3:24139150-24139151	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs150161214	chr3:24139178-24139179	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs375340657	chr3:24139188-24139189	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs548688936	chr3:24139191-24139192	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs183155066	chr3:24139194-24139195	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs570715078	chr3:24139205-24139206	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs568865255	chr3:24139251-24139252	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs12491272	chr3:24139282-24139283	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
50	rs202189290	chr3:24139288-24139289	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	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
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:24137200-24142200	Weak transcription	A549	lung
2	chr3:24137800-24138600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr3:24137800-24139000	Enhancers	Fetal Lung	lung
4	chr3:24137800-24139000	Enhancers	NHDF-Ad	bronchial
5	chr3:24137800-24142800	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr3:24138000-24139000	Enhancers	HSMM	muscle
7	chr3:24138000-24139000	Enhancers	HSMMtube	muscle
8	chr3:24138400-24139000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr3:24138400-24139000	Enhancers	Fetal Stomach	stomach
10	chr3:24138400-24139800	Enhancers	Aorta	Aorta
11	chr3:24138600-24139000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr3:24138600-24139000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr3:24138600-24139000	Enhancers	Fetal Muscle Leg	muscle
14	chr3:24138600-24142200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr3:24139000-24141600	Weak transcription	Fetal Stomach	stomach
16	chr3:24139000-24141800	Weak transcription	Fetal Lung	lung
17	chr3:24139000-24142000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr3:24139000-24142000	Weak transcription	Fetal Muscle Leg	muscle
19	chr3:24139000-24142000	Weak transcription	NHDF-Ad	bronchial
20	chr3:24139000-24142200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr3:24139000-24142200	Weak transcription	HSMM	muscle
22	chr3:24139000-24142800	Weak transcription	HSMMtube	muscle
23	chr3:24139200-24139400	Enhancers	Right Atrium	heart
24	chr3:24139400-24142600	Weak transcription	Right Atrium	heart
25	chr3:24139800-24141000	Weak transcription	Aorta	Aorta

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