Variant report

Variant	rs8080990
Chromosome Location	chr17:59482300-59482301
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:31)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:59482127-59482489	ProgFib	skin:	n/a	n/a
2	SUZ12	chr17:59473583-59483306	NT2-D1	testis:	n/a	n/a
3	HDAC2	chr17:59474717-59482617	MCF-7	breast:	n/a	chr17:59476354-59476363 chr17:59480823-59480832
4	POLR2A	chr17:59482101-59482540	SK-N-SH	brain:	n/a	n/a
5	GATA3	chr17:59480398-59484021	MCF-7	breast:	n/a	n/a
6	POLR2A	chr17:59473262-59482475	IMR90	lung:	n/a	n/a
7	SUZ12	chr17:59477100-59483936	H1-hESC	embryonic stem cell:	n/a	n/a
8	CTBP2	chr17:59480264-59483469	H1-hESC	embryonic stem cell:	n/a	n/a
9	MAX	chr17:59474705-59482813	MCF-7	breast:	n/a	chr17:59480404-59480414 chr17:59475824-59475831 chr17:59479783-59479793 chr17:59480615-59480622
10	TEAD4	chr17:59480991-59483131	A549	lung:	n/a	n/a

No data

(count:31 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:59474707..59482954-chr20:45984179..45991970,21	MCF-7	breast:
2	chr17:58754223..58756511-chr17:59482000..59485280,3	MCF-7	breast:
3	chr17:59480431..59482660-chr17:59485000..59486944,2	K562	blood:
4	chr17:59415713..59496229-chr20:49401322..49431802,760	MCF-7	breast:
5	chr17:59481269..59484457-chr20:49347063..49350762,5	MCF-7	breast:
6	chr17:59481026..59483132-chr20:49287084..49289815,2	MCF-7	breast:
7	chr17:59468469..59482635-chr20:45977748..45992950,51	MCF-7	breast:
8	chr17:59481761..59484680-chr2:208027561..208030537,2	MCF-7	breast:
9	chr17:59481155..59482668-chrX:153598618..153601457,2	MCF-7	breast:
10	chr17:59480732..59482845-chr20:46133657..46135667,2	MCF-7	breast:
11	chr17:59482267..59483832-chr6:27855206..27857614,2	MCF-7	breast:
12	chr17:59481801..59484751-chr19:10097563..10099903,2	MCF-7	breast:
13	chr17:59480994..59483569-chr20:49378333..49381196,2	MCF-7	breast:
14	chr1:121483536..121485359-chr17:59481457..59484090,2	MCF-7	breast:
15	chr17:59481671..59483885-chrX:153625602..153628286,2	MCF-7	breast:
16	chr17:57920470..57923720-chr17:59481457..59485042,3	MCF-7	breast:
17	chr17:59479989..59482835-chr4:105995713..105997792,2	MCF-7	breast:
18	chr17:59480804..59482388-chr20:52726922..52728765,2	MCF-7	breast:
19	chr17:59480537..59483087-chr20:49365408..49367603,2	MCF-7	breast:
20	chr17:59481156..59484305-chr20:48767027..48768757,3	MCF-7	breast:
21	chr1:112530410..112534902-chr17:59481656..59484455,4	MCF-7	breast:
22	chr17:59468167..59483990-chr20:49341590..49352501,35	MCF-7	breast:
23	chr17:59482298..59484810-chr19:42579024..42581918,2	MCF-7	breast:
24	chr17:59474608..59482837-chr20:48728341..48732502,9	MCF-7	breast:
25	chr17:59480348..59483152-chr20:55837594..55839642,2	MCF-7	breast:
26	chr17:59482209..59484444-chr20:45961408..45964255,2	MCF-7	breast:
27	chr17:59481706..59484679-chr3:63742326..63744384,2	MCF-7	breast:
28	chr1:112538021..112540702-chr17:59481732..59483307,2	MCF-7	breast:
29	chr17:59481505..59483109-chr3:64279224..64281674,2	MCF-7	breast:
30	chr17:57913418..57928047-chr17:59480816..59492160,26	MCF-7	breast:
31	chr17:59447417..59500105-chr20:49391742..49424382,639	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000267131	TF binding region
TBX2	TF binding region
ENSG00000171385	Chromatin interaction
ENSG00000141376	Chromatin interaction
ENSG00000124243	Chromatin interaction
ENSG00000124171	Chromatin interaction
ENSG00000231437	Chromatin interaction
ENSG00000273451	Chromatin interaction
ENSG00000231119	Chromatin interaction
ENSG00000121068	Chromatin interaction
ENSG00000201524	Chromatin interaction
ENSG00000105732	Chromatin interaction
ENSG00000196924	Chromatin interaction
ENSG00000147403	Chromatin interaction
ENSG00000244687	Chromatin interaction
ENSG00000118263	Chromatin interaction
ENSG00000101040	Chromatin interaction
ENSG00000199004	Chromatin interaction
ENSG00000062716	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1076393	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1132179	0.84[EUR][1000 genomes]
rs12451524	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2286524	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3744449	0.96[EUR][1000 genomes]
rs3760369	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4455026	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59051236	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7208889	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7214900	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs729782	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs740753	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs740754	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8066348	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8075606	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8078820	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]

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:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:59478000-59485400	Transcr. at gene 5' and 3'	Fetal Lung	lung
2	chr17:59478000-59488200	Transcr. at gene 5' and 3'	NHLF	lung
3	chr17:59478200-59483400	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr17:59478200-59487600	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr17:59478200-59487800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr17:59478600-59486400	Weak transcription	A549	lung
7	chr17:59479000-59486600	Weak transcription	HSMMtube	muscle
8	chr17:59479400-59482400	Bivalent Enhancer	Liver	Liver
9	chr17:59479400-59484000	Active TSS	Ovary	ovary
10	chr17:59479400-59487200	Weak transcription	Hela-S3	cervix
11	chr17:59479600-59483800	Weak transcription	HepG2	liver
12	chr17:59480000-59483000	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
13	chr17:59480200-59482400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
14	chr17:59480200-59483000	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
15	chr17:59480200-59486400	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr17:59480400-59482600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
17	chr17:59480400-59482600	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
18	chr17:59480400-59482600	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
19	chr17:59480400-59482800	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
20	chr17:59480400-59483000	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr17:59480400-59483000	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
22	chr17:59480400-59483400	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
23	chr17:59480400-59483400	Bivalent/Poised TSS	Psoas Muscle	Psoas
24	chr17:59480400-59483600	Transcr. at gene 5' and 3'	Lung	lung
25	chr17:59480400-59484000	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
26	chr17:59480400-59486000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr17:59480400-59486200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr17:59480400-59486400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr17:59480400-59488000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
30	chr17:59480600-59483200	Bivalent Enhancer	Primary B cells from cord blood	blood
31	chr17:59480800-59482400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
32	chr17:59480800-59482400	Strong transcription	Aorta	Aorta
33	chr17:59480800-59483000	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
34	chr17:59480800-59483400	Active TSS	Right Atrium	heart
35	chr17:59481000-59483000	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
36	chr17:59481200-59482600	Bivalent Enhancer	Fetal Thymus	thymus
37	chr17:59481200-59482600	Bivalent Enhancer	Stomach Mucosa	stomach
38	chr17:59481200-59482800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr17:59481200-59482800	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
40	chr17:59481200-59482800	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
41	chr17:59481400-59482400	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
42	chr17:59481400-59482400	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
43	chr17:59481400-59482600	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
44	chr17:59481400-59482600	Flanking Bivalent TSS/Enh	Primary T helper 17 cells PMA-I stimulated	--
45	chr17:59481400-59482600	Bivalent Enhancer	Colon Smooth Muscle	Colon
46	chr17:59481400-59482800	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
47	chr17:59481400-59482800	Flanking Bivalent TSS/Enh	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr17:59481400-59482800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr17:59481400-59482800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr17:59481400-59482800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links