Variant report

Variant	rs887258
Chromosome Location	chr17:59479580-59479581
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:14)
CpG islands
(count:0)
Chromatin interactive
region (count:41)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:14 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:59479337-59479675	H1-neurons	neurons:	n/a	n/a
2	POLR2A	chr17:59468390-59479830	ProgFib	skin:	n/a	n/a
3	SUZ12	chr17:59473583-59483306	NT2-D1	testis:	n/a	n/a
4	MXI1	chr17:59473914-59480739	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr17:59477995-59479760	SK-N-SH	brain:	n/a	n/a
6	HDAC2	chr17:59474717-59482617	MCF-7	breast:	n/a	chr17:59476354-59476363 chr17:59480823-59480832
7	CTBP2	chr17:59478138-59479685	H1-hESC	embryonic stem cell:	n/a	n/a
8	TEAD4	chr17:59474770-59479769	A549	lung:	n/a	n/a
9	POLR2A	chr17:59473262-59482475	IMR90	lung:	n/a	n/a
10	SUZ12	chr17:59477100-59483936	H1-hESC	embryonic stem cell:	n/a	n/a
11	GATA3	chr17:59477741-59479657	MCF-7	breast:	n/a	n/a
12	MAX	chr17:59474705-59482813	MCF-7	breast:	n/a	chr17:59480404-59480414 chr17:59475824-59475831 chr17:59479783-59479793 chr17:59480615-59480622
13	SIN3AK20	chr17:59477976-59479736	SK-N-SH	brain:	n/a	n/a
14	POLR2A	chr17:59479254-59479673	SK-N-SH	brain:	n/a	n/a

No data

(count:41 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:112531992..112535158-chr17:59479505..59481560,4	MCF-7	breast:
2	chr17:59474707..59482954-chr20:45984179..45991970,21	MCF-7	breast:
3	chr10:74036416..74038370-chr17:59477900..59480470,2	MCF-7	breast:
4	chr17:59470038..59471787-chr17:59478375..59480606,2	K562	blood:
5	chr17:59415713..59496229-chr20:49401322..49431802,760	MCF-7	breast:
6	chr17:57914760..57924876-chr17:59472133..59480361,28	MCF-7	breast:
7	chr17:57918266..57925909-chr17:59474699..59479743,11	MCF-7	breast:
8	chr17:59468937..59480240-chr20:49340039..49356868,49	MCF-7	breast:
9	chr1:115053027..115055485-chr17:59479222..59481170,2	MCF-7	breast:
10	chr1:112546090..112547991-chr17:59478108..59480526,2	MCF-7	breast:
11	chr17:59468469..59482635-chr20:45977748..45992950,51	MCF-7	breast:
12	chr17:57929360..57930969-chr17:59478398..59481379,3	MCF-7	breast:
13	chr17:56706858..56710627-chr17:59472052..59479583,11	MCF-7	breast:
14	chr17:59477761..59480587-chr18:812483..814918,2	MCF-7	breast:
15	chr17:59478702..59480576-chr20:49364151..49366179,2	MCF-7	breast:
16	chr17:59478047..59480711-chr7:42997001..42999058,2	MCF-7	breast:
17	chr17:42421591..42424579-chr17:59479495..59481204,2	MCF-7	breast:
18	chr17:59476717..59479924-chr6:6757897..6761293,3	MCF-7	breast:
19	chr17:59476007..59480817-chr20:55837817..55844035,9	MCF-7	breast:
20	chr17:59474584..59479937-chr20:48725175..48731303,15	MCF-7	breast:
21	chr17:59477079..59481029-chr20:46128798..46132223,4	MCF-7	breast:
22	chr17:59479446..59481279-chr20:45807034..45809096,2	MCF-7	breast:
23	chr17:56707939..56709505-chr17:59478696..59480864,2	MCF-7	breast:
24	chr17:59478204..59480463-chr7:1892056..1894919,2	MCF-7	breast:
25	chr1:113160722..113162731-chr17:59478884..59481703,2	MCF-7	breast:
26	chr17:59477651..59479888-chr6:89671941..89673981,2	MCF-7	breast:
27	chr11:65190161..65193929-chr17:59476956..59480011,3	MCF-7	breast:
28	chr17:59478442..59480320-chr2:227663816..227665961,2	MCF-7	breast:
29	chr17:59479348..59480157-chr20:49343779..49344441,2	MCF-7	breast:
30	chr17:59477621..59480570-chr6:27113149..27115368,2	MCF-7	breast:
31	chr17:58037859..58039805-chr17:59478183..59480343,2	MCF-7	breast:
32	chr17:59477291..59479669-chr8:96145065..96147248,2	MCF-7	breast:
33	chr17:59477261..59479812-chr7:115849436..115851792,2	MCF-7	breast:
34	chr17:59474996..59480161-chr20:52556121..52561884,6	MCF-7	breast:
35	chr17:59468167..59483990-chr20:49341590..49352501,35	MCF-7	breast:
36	chr14:52120367..52123357-chr17:59479222..59482219,2	MCF-7	breast:
37	chr17:59474608..59482837-chr20:48728341..48732502,9	MCF-7	breast:
38	chr17:59478175..59480475-chrX:118533975..118535993,2	MCF-7	breast:
39	chr17:59479390..59482015-chr20:52396312..52397841,2	MCF-7	breast:
40	chr17:59477427..59479626-chr17:59488065..59490134,11	MCF-7	breast:
41	chr17:59447417..59500105-chr20:49391742..49424382,639	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000267131	TF binding region
ENSG00000267280	TF binding region
ENSG00000199004	Chromatin interaction
ENSG00000201524	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000135269	Chromatin interaction
ENSG00000062716	Chromatin interaction
ENSG00000224532	Chromatin interaction
ENSG00000176105	Chromatin interaction
ENSG00000244687	Chromatin interaction
ENSG00000101040	Chromatin interaction
ENSG00000124151	Chromatin interaction
ENSG00000231119	Chromatin interaction
ENSG00000226308	Chromatin interaction
ENSG00000116489	Chromatin interaction
ENSG00000111880	Chromatin interaction
ENSG00000175895	Chromatin interaction
ENSG00000007341	Chromatin interaction
ENSG00000236352	Chromatin interaction
ENSG00000101144	Chromatin interaction
ENSG00000273451	Chromatin interaction
ENSG00000124243	Chromatin interaction
ENSG00000272622	Chromatin interaction
ENSG00000030582	Chromatin interaction
ENSG00000187013	Chromatin interaction
ENSG00000267280	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000169047	Chromatin interaction
ENSG00000273355	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000197323	Chromatin interaction
ENSG00000124171	Chromatin interaction
ENSG00000231437	Chromatin interaction
ENSG00000245532	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1476781	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2109019	1.00[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.83[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2286525	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs60261365	0.93[AFR][1000 genomes]
rs7214743	0.94[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs757608	1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs758599	0.83[JPT][hapmap]
rs8064243	0.87[ASN][1000 genomes]
rs882367	0.82[JPT][hapmap]
rs9892365	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9905385	1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs9907379	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065939	chr17:59283350-59517730	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	331 gene(s)	inside rSNPs	diseases
2	nsv833505	chr17:59323466-59518007	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	326 gene(s)	inside rSNPs	diseases
3	nsv833506	chr17:59362377-59562984	Bivalent Enhancer Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
4	nsv518130	chr17:59456589-59491281	Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	265 gene(s)	inside rSNPs	diseases
5	esv1796927	chr17:59460119-59495319	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	270 gene(s)	inside rSNPs	diseases
6	nsv908663	chr17:59464069-59521310	Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	278 gene(s)	inside rSNPs	diseases
7	nsv908664	chr17:59465697-59491030	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	261 gene(s)	inside rSNPs	diseases
8	nsv908665	chr17:59470193-59494574	Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases
9	nsv908666	chr17:59470842-59489822	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	253 gene(s)	inside rSNPs	diseases
10	nsv908667	chr17:59471151-59491030	Flanking Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	256 gene(s)	inside rSNPs	diseases
11	nsv908668	chr17:59471151-59494574	Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	263 gene(s)	inside rSNPs	diseases
12	nsv908669	chr17:59471372-59491030	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Weak transcription Enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	255 gene(s)	inside rSNPs	diseases
13	nsv908670	chr17:59471372-59494574	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	262 gene(s)	inside rSNPs	diseases
14	nsv908671	chr17:59475888-59494574	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	255 gene(s)	inside rSNPs	diseases
15	nsv908672	chr17:59476062-59494574	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	255 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:59473400-59479800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
2	chr17:59474200-59481000	Active TSS	NHDF-Ad	bronchial
3	chr17:59474400-59479800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
4	chr17:59475000-59480400	Bivalent/Poised TSS	Fetal Intestine Small	intestine
5	chr17:59475400-59479600	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
6	chr17:59476200-59479600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr17:59476600-59480600	Active TSS	Right Atrium	heart
8	chr17:59476800-59479600	Active TSS	Pancreas	Pancrea
9	chr17:59477200-59480400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
10	chr17:59477200-59482200	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
11	chr17:59477400-59479800	Bivalent/Poised TSS	Sigmoid Colon	Sigmoid Colon
12	chr17:59477800-59480400	Active TSS	Gastric	stomach
13	chr17:59477800-59482000	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
14	chr17:59478000-59479600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
15	chr17:59478000-59479800	Bivalent/Poised TSS	Psoas Muscle	Psoas
16	chr17:59478000-59480000	Bivalent/Poised TSS	Brain Anterior Caudate	brain
17	chr17:59478000-59485400	Transcr. at gene 5' and 3'	Fetal Lung	lung
18	chr17:59478000-59488200	Transcr. at gene 5' and 3'	NHLF	lung
19	chr17:59478200-59479600	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
20	chr17:59478200-59479800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr17:59478200-59483400	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr17:59478200-59487600	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr17:59478200-59487800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr17:59478400-59479600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
25	chr17:59478400-59479600	Bivalent/Poised TSS	Esophagus	oesophagus
26	chr17:59478400-59479600	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
27	chr17:59478400-59479600	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
28	chr17:59478400-59480400	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr17:59478400-59480400	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
30	chr17:59478400-59480400	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
31	chr17:59478400-59481800	Bivalent/Poised TSS	Fetal Intestine Large	intestine
32	chr17:59478400-59482200	Bivalent/Poised TSS	Left Ventricle	heart
33	chr17:59478600-59479600	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
34	chr17:59478600-59480200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr17:59478600-59480400	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
36	chr17:59478600-59480400	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
37	chr17:59478600-59480600	Bivalent/Poised TSS	Placenta	Placenta
38	chr17:59478600-59481600	Bivalent/Poised TSS	Fetal Kidney	kidney
39	chr17:59478600-59486400	Weak transcription	A549	lung
40	chr17:59478800-59479600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr17:59478800-59479600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr17:59478800-59480000	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
43	chr17:59478800-59480600	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
44	chr17:59479000-59479600	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr17:59479000-59479600	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr17:59479000-59479600	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
47	chr17:59479000-59480200	Bivalent Enhancer	Primary T cells from cord blood	blood
48	chr17:59479000-59480400	Weak transcription	Aorta	Aorta
49	chr17:59479000-59480800	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
50	chr17:59479000-59486600	Weak transcription	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links