Variant report

Variant	nsv537873
Chromosome Location	chr5:115490345-115563533
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	CBX3	chr5:115509774-115510264	HCT-116	colon:	n/a	n/a
2	CBX3	chr5:115511708-115512163	HCT-116	colon:	n/a	n/a
3	CEBPB	chr5:115497905-115498301	HepG2	liver:	n/a	chr5:115498150-115498161
4	CEBPB	chr5:115498007-115498261	Hela-S3	cervix:	n/a	chr5:115498150-115498161
5	CEBPB	chr5:115497969-115498167	K562	blood:	n/a	chr5:115498150-115498161
6	CEBPB	chr5:115511524-115511726	HepG2	liver:	n/a	chr5:115511652-115511663
7	CEBPB	chr5:115511551-115511792	K562	blood:	n/a	chr5:115511652-115511663
8	CEBPB	chr5:115497933-115498209	A549	lung:	n/a	chr5:115498150-115498161
9	CEBPB	chr5:115511494-115511805	IMR90	lung:	n/a	chr5:115511652-115511663
10	CTCF	chr5:115546959-115547004	Spleen_OC	spleen:	n/a	n/a
11	CTCF	chr5:115545600-115545750	HCPEpiC	choroid plexus:	n/a	n/a
12	CTCF	chr5:115514460-115514610	BE2_C	brain:	n/a	n/a
13	CTCF	chr5:115499018-115499081	Fibrobl	skin:	n/a	n/a
14	CTCF	chr5:115514420-115514570	HCPEpiC	choroid plexus:	n/a	n/a
15	CTCF	chr5:115527000-115527150	GM06990	blood:	n/a	n/a
16	CTCF	chr5:115505914-115505969	LNCaP	prostate:	n/a	n/a
17	CTCF	chr5:115495000-115495150	HPAF	blood vessel:	n/a	n/a
18	CTCF	chr5:115563372-115563423	GM13976	blood:	n/a	n/a
19	CTCF	chr5:115526780-115526930	HepG2	liver:	n/a	n/a
20	EBF1	chr5:115553101-115553358	GM12878	blood:	n/a	n/a
21	EP300	chr5:115562218-115562251	K562	blood:	n/a	n/a
22	FOS	chr5:115511876-115512190	MCF10A-Er-Src	breast:	n/a	n/a
23	FOS	chr5:115511882-115512082	MCF10A-Er-Src	breast:	n/a	n/a
24	FOS	chr5:115511871-115512146	MCF10A-Er-Src	breast:	n/a	n/a
25	FOS	chr5:115511949-115512080	MCF10A-Er-Src	breast:	n/a	n/a
26	FOXA1	chr5:115546868-115547069	T-47D	breast:	n/a	n/a
27	FOXA1	chr5:115490693-115490906	HepG2	liver:	n/a	chr5:115490811-115490826
28	FOXA1	chr5:115490653-115491008	HepG2	liver:	n/a	chr5:115490811-115490826
29	FOXA1	chr5:115490663-115490990	HepG2	liver:	n/a	chr5:115490811-115490826
30	FOXA1	chr5:115489965-115490352	HepG2	liver:	n/a	n/a
31	FOXA1	chr5:115490652-115491022	HepG2	liver:	n/a	chr5:115490811-115490826
32	FOXA2	chr5:115546874-115547055	HepG2	liver:	n/a	n/a
33	FOXA2	chr5:115490731-115490893	HepG2	liver:	n/a	n/a
34	GABPA	chr5:115493837-115493993	GM12878	blood:	n/a	n/a
35	GABPA	chr5:115493871-115493987	Hela-S3	cervix:	n/a	n/a
36	GABPA	chr5:115493849-115493999	GM12878	blood:	n/a	n/a
37	GATA2	chr5:115496861-115497155	SH-SY5Y	brain:	n/a	n/a
38	GATA3	chr5:115562600-115562894	SH-SY5Y	brain:	n/a	n/a
39	GATA3	chr5:115496759-115497061	SH-SY5Y	brain:	n/a	n/a
40	GATA3	chr5:115532851-115533266	SK-N-SH	brain:	n/a	n/a
41	GATA3	chr5:115555733-115556106	SH-SY5Y	brain:	n/a	n/a
42	GATA3	chr5:115532827-115533270	SK-N-SH	brain:	n/a	n/a
43	GATA3	chr5:115540807-115540886	SH-SY5Y	brain:	n/a	n/a
44	GATA3	chr5:115532809-115533271	MCF-7	breast:	n/a	n/a
45	GTF2F1	chr5:115527179-115527209	H1-hESC	embryonic stem cell:	n/a	n/a
46	JUN	chr5:115560931-115560946	H1-hESC	embryonic stem cell:	n/a	n/a
47	JUN	chr5:115541691-115541827	HepG2	liver:	n/a	chr5:115541725-115541738
48	JUND	chr5:115554589-115554765	HepG2	liver:	n/a	n/a
49	JUND	chr5:115493860-115494013	HepG2	liver:	n/a	n/a
50	KAP1	chr5:115544780-115545020	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:115473230..115475072-chr5:115489118..115491844,2	MCF-7	breast:
2	chr5:115512590..115515778-chr5:115516651..115520258,3	MCF-7	breast:
3	chr5:115523919..115526832-chr5:115553749..115555427,2	MCF-7	breast:
4	chr5:115523919..115526832-chr5:115553749..115555427,2	MCF-7	breast:
5	chr5:115512590..115515778-chr5:115516651..115520258,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LVRN.1-3	chr5:115549572-115550152	NONHSAT103355
2	lnc-SEMA6A-7	chr5:115553723-115553992	NONHSAT103356

Variant related genes	Relation type
HMGN2P27	TF binding region
RNU6-644P	TF binding region
ENSG00000212457	chromatin interactions
ENSG00000232916	chromatin interactions

Extended variants
information (count: 3920 )
Associated
traits (count: 77 )

Variant overlapped rSNPs/rCNVs (count:3920 , 50 per page) page: 1 2 3 4 5 6 7 ... 79

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs570497443	chr5:115490345-115490346	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs374523370	chr5:115490384-115490385	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs532803909	chr5:115490385-115490386	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs141690373	chr5:115490389-115490390	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs367721545	chr5:115490399-115490400	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs563720072	chr5:115490416-115490417	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs187295790	chr5:115490418-115490419	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs535785415	chr5:115490421-115490422	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs555687639	chr5:115490424-115490425	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs192693631	chr5:115490458-115490459	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs537990639	chr5:115490459-115490460	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs199748612	chr5:115490483-115490484	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs35133023	chr5:115490485-115490486	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs549069221	chr5:115490486-115490487	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs74713275	chr5:115490494-115490495	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs558301097	chr5:115490510-115490511	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs578075330	chr5:115490513-115490514	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs184550033	chr5:115490515-115490516	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs13357632	chr5:115490534-115490535	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
20	rs145460928	chr5:115490542-115490543	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs542923743	chr5:115490555-115490556	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs562796446	chr5:115490598-115490599	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs72804843	chr5:115490615-115490616	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
24	rs35210069	chr5:115490644-115490645	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs529097453	chr5:115490649-115490650	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs36046483	chr5:115490656-115490657	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs2136206	chr5:115490669-115490670	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
28	rs553919837	chr5:115490699-115490700	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs2136207	chr5:115490709-115490710	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
30	rs189467994	chr5:115490737-115490738	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs72804844	chr5:115490772-115490773	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
32	rs6594955	chr5:115490789-115490790	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
33	rs2174996	chr5:115490808-115490809	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
34	rs73253287	chr5:115490826-115490827	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
35	rs549299532	chr5:115490829-115490830	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs569141355	chr5:115490846-115490847	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs547279928	chr5:115490860-115490861	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs568649870	chr5:115490879-115490880	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs192207988	chr5:115490912-115490913	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs113492725	chr5:115490928-115490929	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs147656009	chr5:115490975-115490976	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs184941523	chr5:115490977-115490978	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs553935643	chr5:115490985-115490986	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs189720190	chr5:115491008-115491009	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs536218959	chr5:115491015-115491016	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs556454191	chr5:115491047-115491048	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs576361947	chr5:115491049-115491050	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs56038821	chr5:115491065-115491066	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
49	rs7701528	chr5:115491078-115491079	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
50	rs78453397	chr5:115491088-115491089	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:77)

Disease	PMID	Source
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
Cancer	20164919	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Cancer	16751803	CNVD
Intellectual disability	22102821	CNVD
Breast cancer	17603634	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Melanoma	18172304	CNVD
Glioma	20126413	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
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
Esophageal adenocarcinoma	19417022	CNVD
Barrett''s syndrome	19417022	CNVD
Lung cancer	18438408	CNVD
Bipolar disorder	18458673	CNVD
Thyroid cancer	19087340	CNVD
Breast cancer	21785460	CNVD
Squamous cell cancer	20885788	CNVD
Hepatocellular carcinoma	16750200	CNVD
Neurodevelopmental disorder	22521361	CNVD
Prostate cancer	18632612	CNVD
Breast cancer	17133270	CNVD
Acute myeloid leukemia	20729466	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Acute myeloid leukemia	21251322	CNVD
lymphocytic leukemia	21291569	CNVD
Cancer	20164920	CNVD
Myelodysplastic syndrome	21251322	CNVD
Colorectal cancer	16272173	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Multiple myeloma	17550852	CNVD
Ovarian cancer	21720365	CNVD
Salivary gland tumor	18059337	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Renal cell carcinoma	19377443	CNVD
Prostate cancer	16461572	CNVD
Myelofibrosis	22110671	CNVD
Sezary syndrome	18413736	CNVD
Esophageal squamous carcinoma	17470683	CNVD
Glaucoma	21310917	CNVD
Glioblastoma multiforme	22286061	CNVD
Gastrointestinal stromal cancer	19259404	CNVD
Prostate cancer	22341455	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD
Ependymoma	20639864	CNVD
Congenital anomalies of the kidney and urinary tract	18316590	CNVD

Chromatin state (count:340 , 50 per page) page: 1 2 3 4 5 6 7

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:115462600-115502000	Weak transcription	Fetal Intestine Large	intestine
2	chr5:115468200-115494400	Weak transcription	Primary T cells from cord blood	blood
3	chr5:115468600-115501400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr5:115471600-115521600	Weak transcription	Primary B cells from peripheral blood	blood
5	chr5:115472800-115500200	Weak transcription	Primary B cells from cord blood	blood
6	chr5:115472800-115500400	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr5:115473600-115494800	Weak transcription	Fetal Kidney	kidney
8	chr5:115473600-115495200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr5:115481400-115536000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr5:115484400-115510000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr5:115484400-115521400	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr5:115488400-115501200	Weak transcription	Psoas Muscle	Psoas
13	chr5:115489200-115490800	Enhancers	HepG2	liver
14	chr5:115489200-115491000	Enhancers	Liver	Liver
15	chr5:115489200-115526800	Weak transcription	Pancreas	Pancrea
16	chr5:115489800-115494600	Weak transcription	Fetal Heart	heart
17	chr5:115489800-115528600	Weak transcription	Ovary	ovary
18	chr5:115490000-115491000	Enhancers	Pancreatic Islets	Pancreatic Islet
19	chr5:115490000-115524400	Weak transcription	Left Ventricle	heart
20	chr5:115491600-115492400	Enhancers	Primary neutrophils fromperipheralblood	blood
21	chr5:115492800-115504200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr5:115493000-115493400	Enhancers	HUES48 Cell Line	embryonic stem cell
23	chr5:115493400-115493600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
24	chr5:115493400-115494600	Active TSS	H1 Cell Line	embryonic stem cell
25	chr5:115493600-115494600	Active TSS	HUES48 Cell Line	embryonic stem cell
26	chr5:115493800-115494400	Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr5:115494000-115504400	Weak transcription	Aorta	Aorta
28	chr5:115494400-115495200	Strong transcription	Primary T cells from cord blood	blood
29	chr5:115494600-115495200	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr5:115494600-115495200	Enhancers	HUES48 Cell Line	embryonic stem cell
31	chr5:115494600-115495200	Enhancers	Adipose Nuclei	Adipose
32	chr5:115494600-115495400	Enhancers	Fetal Heart	heart
33	chr5:115494600-115522200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr5:115494800-115495200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr5:115494800-115495400	Enhancers	Fetal Kidney	kidney
36	chr5:115494800-115495400	Enhancers	GM12878-XiMat	blood
37	chr5:115494800-115495800	Enhancers	Brain Substantia Nigra	brain
38	chr5:115495000-115495200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
39	chr5:115495000-115495400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr5:115495000-115495400	Enhancers	Gastric	stomach
41	chr5:115495000-115495400	Enhancers	Spleen	Spleen
42	chr5:115495200-115495400	Enhancers	H1 Cell Line	embryonic stem cell
43	chr5:115495200-115495400	Genic enhancers	Primary T cells from cord blood	blood
44	chr5:115495200-115504600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr5:115495200-115521600	Weak transcription	Adipose Nuclei	Adipose
46	chr5:115495200-115524400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr5:115495400-115496800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr5:115495400-115500600	Weak transcription	Primary T cells from cord blood	blood
49	chr5:115495400-115500600	Weak transcription	GM12878-XiMat	blood
50	chr5:115496800-115497200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links