Variant report

Variant	rs551614360
Chromosome Location	chr4:99580332-99580333
allele	A/T
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	POLR2A	chr4:99579857-99580465	U87	brain:	n/a	n/a
2	TAF1	chr4:99579926-99580351	H1-hESC	embryonic stem cell:	n/a	n/a
3	CTCF	chr4:99580300-99580450	HEEpiC	esophagus:	n/a	n/a
4	CTCF	chr4:99580280-99580430	Caco-2	colon:	n/a	n/a
5	CTCF	chr4:99580300-99580450	NHEK	skin:	n/a	n/a
6	RAD21	chr4:99580153-99580688	A549	lung:	n/a	n/a
7	POLR2A	chr4:99578607-99580432	PBDE	blood:	n/a	n/a
8	RAD21	chr4:99579808-99580675	H1-hESC	embryonic stem cell:	n/a	n/a
9	MAZ	chr4:99578350-99580808	IMR90	lung:	n/a	chr4:99580230-99580240 chr4:99578572-99578581
10	CTCF	chr4:99580300-99580450	AG09309	skin:	n/a	n/a
11	CTCF	chr4:99580320-99580470	HBMEC	blood vessel:	n/a	n/a
12	CTCF	chr4:99580280-99580430	HMEC	breast:	n/a	n/a
13	RAD21	chr4:99577479-99580600	IMR90	lung:	n/a	n/a
14	CTCF	chr4:99580280-99580430	AG04450	lung:	n/a	n/a
15	JUND	chr4:99579992-99580686	H1-hESC	embryonic stem cell:	n/a	chr4:99580172-99580183
16	BACH1	chr4:99580038-99580493	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr4:99579435-99580478	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr4:99578505-99580475	IMR90	lung:	n/a	n/a
19	CTCF	chr4:99580300-99580450	A549	lung:	n/a	n/a
20	POLR2A	chr4:99578464-99580441	HUVEC	blood vessel:	n/a	n/a
21	RAD21	chr4:99579489-99580637	SK-N-SH_RA	brain:	n/a	n/a
22	CTCF	chr4:99580320-99580470	HMEC	breast:	n/a	n/a
23	CTCF	chr4:99580300-99580450	NHDF-neo	bronchial:	n/a	n/a
24	CTCF	chr4:99580200-99580350	NHEK	skin:	n/a	chr4:99580228-99580241
25	TCF7L2	chr4:99579504-99580470	HCT-116	colon:	n/a	n/a
26	CTCF	chr4:99580200-99580350	GM12875	blood:	n/a	chr4:99580228-99580241
27	HA-E2F1	chr4:99578286-99580427	MCF-7	breast:	n/a	chr4:99579866-99579875 chr4:99579557-99579572
28	CTCF	chr4:99580260-99580410	RPTEC	kidney:	n/a	n/a
29	CTCF	chr4:99579864-99580595	IMR90	lung:	n/a	chr4:99580228-99580241
30	CTCF	chr4:99580300-99580450	HVMF	connective:	n/a	n/a
31	CTBP2	chr4:99578768-99580714	H1-hESC	embryonic stem cell:	n/a	n/a
32	MXI1	chr4:99578497-99580630	IMR90	lung:	n/a	n/a
33	RAD21	chr4:99579359-99580713	H1-hESC	embryonic stem cell:	n/a	n/a
34	RAD21	chr4:99580196-99580662	H1-hESC	embryonic stem cell:	n/a	n/a
35	CTCF	chr4:99580260-99580410	MCF-7	breast:	n/a	n/a
36	CHD1	chr4:99580280-99580444	H1-hESC	embryonic stem cell:	n/a	n/a
37	MXI1	chr4:99576467-99580748	SK-N-SH	brain:	n/a	n/a
38	RAD21	chr4:99579654-99580507	SK-N-SH_RA	brain:	n/a	n/a
39	CTCF	chr4:99580280-99580430	HCM	heart:	n/a	n/a
40	CTCF	chr4:99580300-99580450	HRE	kidney:	n/a	n/a
41	CTCF	chr4:99580200-99580350	SK-N-SH_RA	brain:	n/a	chr4:99580228-99580241
42	ZNF143	chr4:99579680-99580594	H1-hESC	embryonic stem cell:	n/a	chr4:99579918-99579928
43	CTCF	chr4:99580331-99580533	A549	lung:	n/a	n/a
44	TBP	chr4:99579361-99580624	H1-hESC	embryonic stem cell:	n/a	n/a
45	RCOR1	chr4:99577675-99581955	IMR90	lung:	n/a	n/a
46	CTCF	chr4:99580280-99580490	HUVEC	blood vessel:	n/a	n/a
47	CTCF	chr4:99579876-99580487	GM12878	blood:	n/a	chr4:99580228-99580241
48	CTCF	chr4:99580320-99580470	WERI-Rb-1	eye:	n/a	n/a
49	SIN3A	chr4:99578902-99580721	H1-hESC	embryonic stem cell:	n/a	chr4:99579506-99579517
50	MAX	chr4:99579285-99580375	H1-hESC	embryonic stem cell:	n/a	chr4:99580230-99580240

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:99180743..99183219-chr4:99577927..99581407,3	MCF-7	breast:
2	chr4:99181647..99184072-chr4:99579310..99582613,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RAP1GDS1-3	chr4:99580055-99585701	ENSG00000260641.1
2	lnc-RAP1GDS1-3	chr4:99580055-99585702	NONHSAT097492

Variant related genes	Relation type
TSPAN5	TF binding region
ENSG00000214559	Chromatin interaction
ENSG00000138698	Chromatin interaction

Extended variants
information (count: 2 )
Associated
traits (count: 0)

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv966532	chr4:99571460-99581225	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	esv3344423	chr4:99578554-99581102	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99576600-99580800	Weak transcription	Hela-S3	cervix
2	chr4:99576800-99580400	Active TSS	NHLF	lung
3	chr4:99577000-99580400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr4:99577200-99580600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr4:99577200-99580600	Active TSS	Brain Angular Gyrus	brain
6	chr4:99577200-99580600	Active TSS	NHDF-Ad	bronchial
7	chr4:99577400-99580400	Active TSS	Cortex derived primary cultured neurospheres	brain
8	chr4:99577400-99580400	Active TSS	HSMM	muscle
9	chr4:99577400-99580600	Active TSS	Brain Inferior Temporal Lobe	brain
10	chr4:99577400-99580800	Active TSS	Ovary	ovary
11	chr4:99577600-99580400	Active TSS	Brain Cingulate Gyrus	brain
12	chr4:99577600-99580400	Active TSS	Brain Hippocampus Middle	brain
13	chr4:99577600-99580600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr4:99577600-99580600	Active TSS	Fetal Brain Female	brain
15	chr4:99577600-99580800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
16	chr4:99577800-99580400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
17	chr4:99577800-99580400	Active TSS	Muscle Satellite Cultured Cells	--
18	chr4:99577800-99580600	Active TSS	HSMMtube	muscle
19	chr4:99578000-99580600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr4:99578000-99580600	Active TSS	Right Atrium	heart
21	chr4:99578000-99580800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
22	chr4:99578000-99581000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
23	chr4:99578200-99580400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr4:99578200-99580400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
25	chr4:99578200-99580400	Active TSS	Osteobl	bone
26	chr4:99578200-99580600	Active TSS	A549	lung
27	chr4:99578200-99580800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
28	chr4:99578200-99581000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
29	chr4:99578400-99580400	Active TSS	Breast Myoepithelial Primary Cells	Breast
30	chr4:99578400-99580400	Active TSS	Fetal Kidney	kidney
31	chr4:99578400-99580600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr4:99578400-99580600	Active TSS	Spleen	Spleen
33	chr4:99578400-99580800	Active TSS	Aorta	Aorta
34	chr4:99578600-99580400	Active TSS	Left Ventricle	heart
35	chr4:99578600-99580600	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
36	chr4:99578600-99580600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
37	chr4:99578600-99580800	Active TSS	Colon Smooth Muscle	Colon
38	chr4:99578600-99580800	Active TSS	Pancreatic Islets	Pancreatic Islet
39	chr4:99578800-99580400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr4:99578800-99580400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr4:99578800-99580400	Active TSS	Sigmoid Colon	Sigmoid Colon
42	chr4:99578800-99580600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr4:99578800-99580800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr4:99578800-99580800	Active TSS	Right Ventricle	heart
45	chr4:99578800-99581000	Active TSS	Esophagus	oesophagus
46	chr4:99579000-99580400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr4:99579000-99580400	Active TSS	Pancreas	Pancrea
48	chr4:99579000-99580400	Active TSS	Psoas Muscle	Psoas
49	chr4:99579000-99580400	Active TSS	Stomach Mucosa	stomach
50	chr4:99579000-99580600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links