Variant report

Variant	rs4699359
Chromosome Location	chr4:99580705-99580706
allele	A/G
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	CTCF	chr4:99580580-99580730	BJ	skin:	n/a	n/a
2	MAZ	chr4:99578350-99580808	IMR90	lung:	n/a	chr4:99580230-99580240 chr4:99578572-99578581
3	CTBP2	chr4:99578768-99580714	H1-hESC	embryonic stem cell:	n/a	n/a
4	RAD21	chr4:99579359-99580713	H1-hESC	embryonic stem cell:	n/a	n/a
5	MXI1	chr4:99576467-99580748	SK-N-SH	brain:	n/a	n/a
6	RCOR1	chr4:99577675-99581955	IMR90	lung:	n/a	n/a
7	SIN3A	chr4:99578902-99580721	H1-hESC	embryonic stem cell:	n/a	chr4:99579506-99579517
8	ZNF263	chr4:99578581-99580952	HEK293-T-REx	kidney:	n/a	n/a
9	CHD2	chr4:99580022-99580730	H1-hESC	embryonic stem cell:	n/a	n/a
10	REST	chr4:99577373-99580795	H1-neurons	neurons:	n/a	chr4:99580193-99580206 chr4:99580562-99580571

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: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12507322	1.00[CHB][hapmap]
rs12512460	0.96[ASN][1000 genomes]
rs12512621	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17027889	1.00[CHB][hapmap];0.88[CHD][hapmap];0.89[MEX][hapmap];0.81[AMR][1000 genomes]
rs1881449	1.00[JPT][hapmap]

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:114 , 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	chr4:99577400-99580800	Active TSS	Ovary	ovary
3	chr4:99577600-99580800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
4	chr4:99578000-99580800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
5	chr4:99578000-99581000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
6	chr4:99578200-99580800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
7	chr4:99578200-99581000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
8	chr4:99578400-99580800	Active TSS	Aorta	Aorta
9	chr4:99578600-99580800	Active TSS	Colon Smooth Muscle	Colon
10	chr4:99578600-99580800	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr4:99578800-99580800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr4:99578800-99580800	Active TSS	Right Ventricle	heart
13	chr4:99578800-99581000	Active TSS	Esophagus	oesophagus
14	chr4:99579000-99580800	Active TSS	H9 Cell Line	embryonic stem cell
15	chr4:99579000-99580800	Active TSS	Gastric	stomach
16	chr4:99579000-99580800	Active TSS	Rectal Mucosa Donor 31	rectum
17	chr4:99579200-99580800	Active TSS	Rectal Smooth Muscle	rectum
18	chr4:99579400-99580800	Active TSS	H1 Cell Line	embryonic stem cell
19	chr4:99579400-99580800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr4:99579600-99580800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr4:99580000-99580800	Flanking Active TSS	Primary T cells from cord blood	blood
22	chr4:99580000-99580800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
23	chr4:99580000-99580800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr4:99580000-99580800	Flanking Active TSS	Duodenum Mucosa	Duodenum
25	chr4:99580000-99580800	Flanking Active TSS	Placenta	Placenta
26	chr4:99580000-99580800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
27	chr4:99580000-99580800	Flanking Active TSS	Stomach Smooth Muscle	stomach
28	chr4:99580000-99581000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr4:99580200-99580800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr4:99580200-99580800	Flanking Active TSS	Primary hematopoietic stem cells	blood
31	chr4:99580200-99580800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
32	chr4:99580200-99580800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr4:99580200-99580800	Flanking Active TSS	Liver	Liver
34	chr4:99580200-99580800	Flanking Active TSS	Brain Anterior Caudate	brain
35	chr4:99580200-99580800	Flanking Active TSS	Brain Germinal Matrix	brain
36	chr4:99580200-99580800	Flanking Active TSS	Fetal Brain Male	brain
37	chr4:99580200-99580800	Flanking Active TSS	Fetal Intestine Large	intestine
38	chr4:99580200-99580800	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
39	chr4:99580200-99580800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
40	chr4:99580200-99580800	Flanking Active TSS	HUVEC	blood vessel
41	chr4:99580200-99581000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr4:99580200-99581000	Flanking Active TSS	HMEC	breast
43	chr4:99580200-99581200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
44	chr4:99580200-99581200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
45	chr4:99580200-99581200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr4:99580200-99581200	Flanking Active TSS	Fetal Stomach	stomach
47	chr4:99580200-99581400	Flanking Active TSS	NH-A	brain
48	chr4:99580200-99581400	Flanking Active TSS	NHEK	skin
49	chr4:99580200-99581600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr4:99580200-99581600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--

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