Variant report

Variant	nsv328503
Chromosome Location	chr5:61855770-61857102
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	CUX1	chr5:61856062-61856151	K562	blood:	n/a	n/a
2	EP300	chr5:61856393-61857090	SK-N-SH_RA	brain:	n/a	n/a
3	EP300	chr5:61856478-61857063	SK-N-SH_RA	brain:	n/a	n/a
4	EP300	chr5:61856130-61857207	SK-N-SH	brain:	n/a	chr5:61857127-61857137
5	EP300	chr5:61856439-61857100	SK-N-SH	brain:	n/a	n/a
6	GATA3	chr5:61856521-61857128	SK-N-SH	brain:	n/a	n/a
7	GATA3	chr5:61856491-61857228	SK-N-SH	brain:	n/a	n/a
8	MYC	chr5:61856288-61856455	H1-hESC	embryonic stem cell:	n/a	n/a
9	PBX3	chr5:61856466-61857124	SK-N-SH	brain:	n/a	n/a
10	PBX3	chr5:61856449-61857112	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr5:61856627-61856856	SK-N-SH	brain:	n/a	n/a
12	POLR2A	chr5:61856524-61856990	SK-N-SH	brain:	n/a	n/a
13	STAT3	chr5:61857003-61857046	MCF10A-Er-Src	breast:	n/a	n/a
14	TCF12	chr5:61856399-61857176	SK-N-SH	brain:	n/a	n/a
15	TCF12	chr5:61856440-61857129	SK-N-SH	brain:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LRRC70-1	chr5:61856963-61857084	NONHSAT101713
2	lnc-LRRC70-1	chr5:61856523-61856832	NONHSAT101713

Variant related genes	Relation type
IPO11	TF binding region

Extended variants
information (count: 52 )
Associated
traits (count: 93 )

Variant overlapped rSNPs/rCNVs (count:52 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs59563489	chr5:61855770-61855771	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs561834402	chr5:61855776-61855777	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs572170790	chr5:61855778-61855779	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs541178465	chr5:61855870-61855871	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs368835494	chr5:61855893-61855894	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs183169783	chr5:61855904-61855905	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs549403591	chr5:61855939-61855940	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs562929201	chr5:61855951-61855952	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs73108051	chr5:61855952-61855953	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
10	rs552472647	chr5:61856055-61856056	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs566326663	chr5:61856080-61856081	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
12	rs528688434	chr5:61856110-61856111	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
13	rs187535050	chr5:61856131-61856132	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
14	rs568508075	chr5:61856132-61856133	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
15	rs32164	chr5:61856156-61856157	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
16	rs192069486	chr5:61856235-61856236	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
17	rs150200966	chr5:61856257-61856258	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
18	rs539816371	chr5:61856275-61856276	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
19	rs558898241	chr5:61856309-61856310	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
20	rs572255266	chr5:61856336-61856337	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
21	rs138733759	chr5:61856337-61856338	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
22	rs149341643	chr5:61856413-61856414	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
23	rs144893253	chr5:61856513-61856514	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
24	rs543091321	chr5:61856524-61856525	Weak transcription Strong transcription	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
25	rs528631302	chr5:61856546-61856547	Weak transcription Strong transcription	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
26	rs531994746	chr5:61856549-61856550	Weak transcription Strong transcription	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
27	rs185020929	chr5:61856566-61856567	Weak transcription Strong transcription	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
28	rs556868734	chr5:61856609-61856610	Weak transcription Strong transcription	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
29	rs574888993	chr5:61856615-61856616	Weak transcription Strong transcription	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
30	rs559799840	chr5:61856657-61856658	Weak transcription Strong transcription	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
31	rs528779243	chr5:61856683-61856684	Weak transcription Strong transcription	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
32	rs548539710	chr5:61856709-61856710	Weak transcription Strong transcription	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
33	rs540360335	chr5:61856721-61856722	Weak transcription Strong transcription	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
34	rs112540291	chr5:61856758-61856759	Weak transcription Strong transcription	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
35	rs531056894	chr5:61856795-61856796	Weak transcription Strong transcription	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
36	rs375139405	chr5:61856875-61856876	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
37	rs115678363	chr5:61856886-61856887	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
38	rs138727887	chr5:61856922-61856923	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
39	rs141796093	chr5:61856925-61856926	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
40	rs200514803	chr5:61856946-61856947	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
41	rs542831986	chr5:61856947-61856948	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
42	rs564970800	chr5:61856948-61856949	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
43	rs368095879	chr5:61856950-61856951	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
44	rs534899503	chr5:61856952-61856953	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
45	rs146240342	chr5:61856986-61856987	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
46	rs368418025	chr5:61857012-61857013	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
47	rs188277939	chr5:61857044-61857045	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
48	rs148438020	chr5:61857047-61857048	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
49	rs371653354	chr5:61857061-61857062	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
50	rs145750694	chr5:61857063-61857064	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a

Variant related diseases (count:93)

Disease	PMID	Source
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Metanephric adenoma	20802469	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Medulloblastoma	21979893	CNVD
Phyllodes tumor	17334353	CNVD
Malaria	21533027	CNVD
Renal cell carcinoma	19461508	CNVD
Colorectal cancer	21645411	CNVD
Gastric cancer	22152101	CNVD
Oesophago-gastric ulcer	22152101	CNVD
Ovarian cancer	21781307	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Lung cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Cancer	20164919	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Multiple myeloma	17550852	CNVD
Thoracic aortic aneurysm	21092924	CNVD
DNA damage stimulus	22844521	CNVD
DNA repair	22844521	CNVD
Breast cancer	21785460	CNVD
Spinal muscular atrophy	22422766	CNVD
Spinal muscular atrophy	22558076	CNVD
Spinal muscular atrophy	21320981	CNVD
Spinal muscular atrophy	21762474	CNVD
Cancer	16751803	CNVD
Intellectual disability	22102821	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Breast cancer	17603634	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Melanoma	18172304	CNVD
Glioma	20126413	CNVD
Non-small cell lung cancer	21829676	CNVD
Breast cancer	22032731	CNVD
Prostate cancer	21965145	CNVD
Esophageal cancer	20955586	CNVD
Congenital anomalies of the kidney and urinary tract	18694510	CNVD
Ovarian cancer	20844748	CNVD
Breast cancer	17393978	CNVD
Cancer	21359685	CNVD
adenomatous polyposis	22470819	CNVD
Cancer	22429812	CNVD
Cancer	21637783	CNVD
Colorectal cancer	20709793	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Liposarcoma	21253554	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	17387387	CNVD
Breast cancer	21858162	CNVD
Hepatocellular carcinoma	16750200	CNVD
Leukemia	17361228	CNVD
Myelodysplastic syndrome	18508791	CNVD
5q-syndrome	17576883	CNVD
Gastric cancer	17908304	CNVD
Lung cancer	16740712	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Urothelial carcinoma	21177765	CNVD
Acute myeloid leukemia	20729466	CNVD
Acute myeloid leukemia	21251322	CNVD
Oral cancer	21386901	CNVD
Bladder cancer	21909424	CNVD
Esophageal adenocarcinoma	19417022	CNVD
Barrett''s syndrome	19417022	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Breast cancer	17133270	CNVD
Breast cancer	19602461	CNVD
Renal cell carcinoma	18194544	CNVD
abnormal development	18461090	CNVD
Esophageal adenocarcinoma	18519675	CNVD
Retinoblastoma	22278416	CNVD
Bipolar disorder	18458673	CNVD
Thyroid cancer	19087340	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Breast cancer	21364760	CNVD
Colorectal cancer	16774939	CNVD
Myelofibrosis	22110671	CNVD
Neuroticism	17667963	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:61739200-61862800	Weak transcription	Brain Substantia Nigra	brain
2	chr5:61748000-61862800	Weak transcription	Right Ventricle	heart
3	chr5:61758800-61890000	Weak transcription	Small Intestine	intestine
4	chr5:61764000-61858200	Weak transcription	Placenta	Placenta
5	chr5:61764200-61895800	Weak transcription	Pancreas	Pancrea
6	chr5:61771200-61864800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr5:61771400-61863000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr5:61781600-61867600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr5:61787400-61866800	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr5:61793600-61905000	Weak transcription	NHEK	skin
11	chr5:61796600-61866600	Weak transcription	Osteobl	bone
12	chr5:61796800-61899000	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr5:61797000-61861200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr5:61802600-61889000	Weak transcription	NH-A	brain
15	chr5:61803000-61904400	Weak transcription	Fetal Kidney	kidney
16	chr5:61803200-61875000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr5:61803400-61863600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr5:61804400-61865200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr5:61806800-61863400	Weak transcription	Lung	lung
20	chr5:61812200-61865200	Weak transcription	HUVEC	blood vessel
21	chr5:61815000-61861400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr5:61815200-61890600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr5:61816000-61857800	Weak transcription	Fetal Stomach	stomach
24	chr5:61816200-61862200	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr5:61819200-61860400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr5:61819800-61861600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr5:61821400-61863400	Weak transcription	Aorta	Aorta
28	chr5:61823200-61856000	Weak transcription	Fetal Heart	heart
29	chr5:61827200-61856000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr5:61827200-61858200	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr5:61827200-61861200	Weak transcription	Liver	Liver
32	chr5:61827200-61883600	Weak transcription	HepG2	liver
33	chr5:61827400-61862800	Weak transcription	Stomach Smooth Muscle	stomach
34	chr5:61827400-61899200	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr5:61827600-61856000	Weak transcription	Fetal Thymus	thymus
36	chr5:61828200-61855800	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr5:61828200-61861600	Weak transcription	Brain Hippocampus Middle	brain
38	chr5:61828200-61862800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr5:61828200-61864400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr5:61828200-61886800	Weak transcription	Duodenum Mucosa	Duodenum
41	chr5:61828600-61858000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr5:61828600-61861600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr5:61830400-61856000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr5:61831400-61871800	Weak transcription	Psoas Muscle	Psoas
45	chr5:61834200-61861400	Weak transcription	GM12878-XiMat	blood
46	chr5:61834800-61858200	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr5:61834800-61858200	Weak transcription	Fetal Brain Female	brain
48	chr5:61834800-61861000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr5:61834800-61861600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr5:61834800-61864600	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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