Variant report

Variant	rs59233561
Chromosome Location	chr6:28725415-28725416
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:24)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:24 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28695559..28699343-chr6:28721391..28727067,6	K562	blood:
2	chr6:28670960..28673190-chr6:28724668..28726201,2	K562	blood:
3	chr6:28676549..28680840-chr6:28724202..28726516,6	K562	blood:
4	chr6:28723357..28725477-chr6:28861527..28864312,2	K562	blood:
5	chr6:28723896..28728359-chr6:28734827..28738855,4	K562	blood:
6	chr6:28692707..28694832-chr6:28724756..28727492,3	K562	blood:
7	chr6:28724691..28726278-chr6:28843409..28846175,2	K562	blood:
8	chr6:28704393..28708100-chr6:28724005..28727294,4	K562	blood:
9	chr6:28722382..28725655-chr6:28783034..28786428,3	K562	blood:
10	chr6:28706832..28708574-chr6:28723413..28725632,2	K562	blood:
11	chr6:28704284..28707045-chr6:28723983..28725942,2	MCF-7	breast:
12	chr6:28723977..28727923-chr6:28779903..28783132,3	K562	blood:
13	chr6:28700497..28703412-chr6:28724677..28728589,3	K562	blood:
14	chr6:28723896..28728359-chr6:28734827..28738855,6	K562	blood:
15	chr6:28723907..28726622-chr6:28947645..28950512,2	K562	blood:
16	chr6:28724813..28727063-chr6:28829378..28832133,3	K562	blood:
17	chr6:28695145..28698066-chr6:28723238..28727067,5	K562	blood:
18	chr6:28724879..28727227-chr6:28741838..28744076,3	K562	blood:
19	chr6:28724259..28726236-chr6:28749088..28750915,2	K562	blood:
20	chr6:28724879..28727227-chr6:28741838..28744076,2	K562	blood:
21	chr6:28676549..28680032-chr6:28724574..28727425,3	K562	blood:
22	chr6:28712043..28717130-chr6:28723838..28729658,8	K562	blood:
23	chr6:28724345..28725903-chr6:28805284..28806800,2	K562	blood:
24	chr6:28723125..28726078-chr6:28775767..28777359,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000224157	Chromatin interaction
ENSG00000225173	Chromatin interaction
ENSG00000221191	Chromatin interaction
ENSG00000225595	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10498733	0.95[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs1107160	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1233582	0.81[ASN][1000 genomes]
rs17280797	0.95[AFR][1000 genomes]
rs17280818	0.95[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs17281186	0.95[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs17398081	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1891757	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs1936180	0.95[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs3999045	0.84[AMR][1000 genomes]
rs55641015	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55659253	0.90[AMR][1000 genomes]
rs55764335	0.90[AMR][1000 genomes]
rs55891766	0.95[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs56003969	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56098960	0.90[AMR][1000 genomes]
rs56165011	0.90[AMR][1000 genomes]
rs56296645	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56384403	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs57170714	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57693980	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs57748269	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57791058	0.90[AMR][1000 genomes]
rs57965355	0.90[AMR][1000 genomes]
rs58104924	0.95[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs58238888	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs58258185	0.90[AMR][1000 genomes]
rs58288624	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59475656	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59959723	0.95[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs60252686	0.90[AMR][1000 genomes]
rs60311527	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs61094745	0.95[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs61208746	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs61657599	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61703239	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6909960	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs6916286	0.86[AMR][1000 genomes]
rs6923795	0.90[AMR][1000 genomes]
rs7742889	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7748319	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7751451	0.90[AMR][1000 genomes]
rs7751884	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs7755641	0.95[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs7758798	0.90[AMR][1000 genomes]
rs7760656	0.95[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs7765829	0.95[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs7766599	0.95[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs7772111	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs7772373	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7772482	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7772682	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs9688414	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs9767343	0.82[AMR][1000 genomes]
rs9767359	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534089	chr6:28636972-28841640	Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28724000-28726400	Active TSS	Hela-S3	cervix
2	chr6:28724600-28726800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
3	chr6:28724800-28726200	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr6:28724800-28726600	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr6:28724800-28726600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
6	chr6:28724800-28726800	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr6:28725000-28725600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr6:28725000-28726000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr6:28725000-28726200	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr6:28725000-28726400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr6:28725000-28726400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr6:28725000-28726600	Active TSS	H1 Cell Line	embryonic stem cell
13	chr6:28725000-28726600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
14	chr6:28725000-28726600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr6:28725000-28726600	Active TSS	K562	blood
16	chr6:28725000-28726800	Active TSS	H9 Cell Line	embryonic stem cell
17	chr6:28725000-28726800	Active TSS	A549	lung
18	chr6:28725000-28726800	Active TSS	HMEC	breast
19	chr6:28725200-28725600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr6:28725200-28726000	Flanking Active TSS	Placenta	Placenta
21	chr6:28725200-28726200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr6:28725200-28726200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr6:28725200-28726200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr6:28725200-28726200	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr6:28725200-28726200	Active TSS	NHEK	skin
26	chr6:28725200-28726400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
27	chr6:28725400-28725600	Bivalent/Poised TSS	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr6:28725400-28726000	Flanking Bivalent TSS/Enh	HepG2	liver
29	chr6:28725400-28726200	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr6:28725400-28726200	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr6:28725400-28726400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links