Variant report

Variant	rs523487
Chromosome Location	chr5:179221149-179221150
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:27)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:27 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:179220619-179221492	GM12891	blood:	n/a	n/a
2	POLR2A	chr5:179221024-179224534	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr5:179220541-179221421	GM12878	blood:	n/a	n/a
4	POLR2A	chr5:179220694-179221265	HepG2	liver:	n/a	n/a
5	POLR2A	chr5:179220797-179221332	GM12892	blood:	n/a	n/a
6	SPI1	chr5:179220512-179221226	HL-60	blood:	n/a	n/a
7	MYC	chr5:179220412-179221233	NB4	blood:	n/a	n/a
8	PAX5	chr5:179220638-179221198	GM12878	blood:	n/a	n/a
9	POLR2A	chr5:179220820-179221217	HUVEC	blood vessel:	n/a	n/a
10	POLR2A	chr5:179221061-179221380	K562	blood:	n/a	n/a
11	POLR2A	chr5:179220253-179221456	HL-60	blood:	n/a	n/a
12	POLR2A	chr5:179220422-179223040	GM12892	blood:	n/a	n/a
13	POLR2A	chr5:179221113-179221425	K562	blood:	n/a	n/a
14	POLR2A	chr5:179220875-179221261	ECC-1	luminal epithelium:	n/a	n/a
15	POLR2A	chr5:179220303-179221219	GM12878	blood:	n/a	n/a
16	POLR2A	chr5:179221107-179221170	MCF10A-Er-Src	breast:	n/a	n/a
17	POLR2A	chr5:179218996-179221960	HL-60	blood:	n/a	n/a
18	POLR2A	chr5:179220355-179221883	H1-neurons	neurons:	n/a	n/a
19	POLR2A	chr5:179220585-179221260	NB4	blood:	n/a	n/a
20	POLR2A	chr5:179220652-179221242	GM12878	blood:	n/a	n/a
21	POLR2A	chr5:179221143-179221151	MCF-7	breast:	n/a	n/a
22	MAX	chr5:179219615-179221657	NB4	blood:	n/a	n/a
23	POLR2A	chr5:179220850-179224671	K562	blood:	n/a	n/a
24	POLR2A	chr5:179220519-179221327	GM12878	blood:	n/a	n/a
25	POLR2A	chr5:179220665-179221262	ECC-1	luminal epithelium:	n/a	n/a
26	POLR2A	chr5:179220594-179221376	SK-N-MC	brain:	n/a	n/a
27	POLR2A	chr5:179219447-179224493	HepG2	liver:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:179157523..179162988-chr5:179219694..179224698,13	MCF-7	breast:
2	chr5:179158179..179161014-chr5:179220671..179223680,5	MCF-7	breast:
3	chr5:179126009..179127718-chr5:179220885..179222493,2	K562	blood:
4	chr5:179123773..179127716-chr5:179220848..179225521,8	MCF-7	breast:
5	chr5:179104067..179106595-chr5:179220718..179223236,3	MCF-7	breast:
6	chr5:179192680..179196164-chr5:179217971..179221244,3	MCF-7	breast:
7	chr5:179124990..179127718-chr5:179220717..179222385,2	K562	blood:

No data

Variant related genes	Relation type
LTC4S	TF binding region
ENSG00000127022	Chromatin interaction
ENSG00000161021	Chromatin interaction
ENSG00000225051	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949554	chr5:178832325-179309513	Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
2	nsv883270	chr5:178951106-179350387	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
3	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases
4	nsv469579	chr5:179184831-179360191	Genic enhancers Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
5	nsv883274	chr5:179186397-179310330	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
6	nsv518964	chr5:179193598-179227286	Strong transcription Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	151 gene(s)	inside rSNPs	diseases
7	nsv883275	chr5:179193598-179267783	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	176 gene(s)	inside rSNPs	diseases
8	nsv883276	chr5:179193598-179310330	Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
9	nsv883277	chr5:179193598-179350387	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
10	nsv823361	chr5:179213324-179251243	Genic enhancers Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	173 gene(s)	inside rSNPs	diseases
11	nsv600659	chr5:179214251-179225594	Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	147 gene(s)	inside rSNPs	diseases
12	nsv600660	chr5:179214251-179231248	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	149 gene(s)	inside rSNPs	diseases
13	nsv883278	chr5:179214818-179238794	Active TSS Genic enhancers Strong transcription Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	154 gene(s)	inside rSNPs	diseases
14	nsv883279	chr5:179214818-179248774	Enhancers Strong transcription Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	173 gene(s)	inside rSNPs	diseases
15	nsv870188	chr5:179218824-179235424	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	154 gene(s)	inside rSNPs	diseases
16	nsv600661	chr5:179220010-179228623	Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	149 gene(s)	inside rSNPs	diseases
17	nsv600662	chr5:179220010-179231248	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	149 gene(s)	inside rSNPs	diseases
18	nsv883280	chr5:179220010-179238794	Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	154 gene(s)	inside rSNPs	diseases
19	nsv883281	chr5:179220010-179250500	Active TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	173 gene(s)	inside rSNPs	diseases
20	nsv883282	chr5:179220638-179231248	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	149 gene(s)	inside rSNPs	diseases
21	nsv883283	chr5:179220638-179231681	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	149 gene(s)	inside rSNPs	diseases
22	nsv883284	chr5:179220638-179246415	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	158 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179202000-179221800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr5:179203400-179221600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr5:179203600-179222000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr5:179204000-179221200	Weak transcription	Small Intestine	intestine
5	chr5:179205200-179221800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr5:179207600-179221200	Weak transcription	Fetal Intestine Large	intestine
7	chr5:179207600-179222200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr5:179207600-179222600	Weak transcription	Aorta	Aorta
9	chr5:179207800-179222200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr5:179209400-179222200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr5:179209600-179221600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr5:179215600-179221200	Weak transcription	Thymus	Thymus
13	chr5:179215600-179223200	Weak transcription	HSMMtube	muscle
14	chr5:179218600-179221600	Enhancers	Placenta	Placenta
15	chr5:179218600-179222800	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr5:179218800-179222000	Enhancers	Liver	Liver
17	chr5:179219000-179221400	Enhancers	Spleen	Spleen
18	chr5:179219200-179221800	Enhancers	HepG2	liver
19	chr5:179219400-179221200	Enhancers	Lung	lung
20	chr5:179219400-179222200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr5:179219400-179222400	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr5:179219400-179222400	Enhancers	Primary B cells from cord blood	blood
23	chr5:179219600-179222400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr5:179219600-179222400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr5:179219600-179222800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr5:179219800-179221800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
27	chr5:179219800-179222200	Weak transcription	Fetal Brain Female	brain
28	chr5:179220000-179221200	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr5:179220000-179221600	Enhancers	Fetal Heart	heart
30	chr5:179220000-179221800	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr5:179220000-179222200	Enhancers	Fetal Lung	lung
32	chr5:179220000-179223000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr5:179220200-179221400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr5:179220200-179221400	Enhancers	Brain Cingulate Gyrus	brain
35	chr5:179220200-179221600	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr5:179220200-179221600	Enhancers	Gastric	stomach
37	chr5:179220200-179222000	Enhancers	Primary T killer memory cells from peripheral blood	blood
38	chr5:179220200-179222000	Enhancers	GM12878-XiMat	blood
39	chr5:179220200-179222200	Enhancers	H1 Cell Line	embryonic stem cell
40	chr5:179220200-179222200	Weak transcription	Brain Germinal Matrix	brain
41	chr5:179220200-179222200	Enhancers	Pancreas	Pancrea
42	chr5:179220200-179222200	Enhancers	Stomach Mucosa	stomach
43	chr5:179220200-179222400	Enhancers	Primary T cells from cord blood	blood
44	chr5:179220200-179222400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr5:179220200-179223800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
46	chr5:179220400-179221200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr5:179220400-179221200	Enhancers	Fetal Thymus	thymus
48	chr5:179220400-179221200	Enhancers	NH-A	brain
49	chr5:179220400-179221400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
50	chr5:179220400-179221400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links