Variant report

Variant	rs11960459
Chromosome Location	chr5:89900718-89900719
allele	C/G
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:89735291..89736086-chr5:89900052..89900990,6	MCF-7	breast:
2	chr5:89899238..89902193-chr5:89950994..89956361,5	K562	blood:
3	chr5:89735670..89736479-chr5:89900164..89900970,2	K562	blood:
4	chr5:89704196..89707423-chr5:89899106..89902473,4	K562	blood:
5	chr5:89853355..89855789-chr5:89900091..89901923,2	MCF-7	breast:
6	chr5:89899642..89902183-chr5:89950994..89955309,3	K562	blood:
7	chr5:89825636..89826384-chr5:89900047..89900941,2	K562	blood:
8	chr5:89767614..89772956-chr5:89898929..89905987,8	K562	blood:
9	chr5:89900245..89902488-chr5:89903253..89905685,5	K562	blood:
10	chr5:89737219..89738135-chr5:89899968..89900731,2	MCF-7	breast:
11	chr5:89823952..89826315-chr5:89899219..89901608,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000113356	Chromatin interaction
ENSG00000176055	Chromatin interaction
ENSG00000255647	Chromatin interaction
ENSG00000164199	Chromatin interaction
ENSG00000176018	Chromatin interaction
ENSG00000153140	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11948077	1.00[EUR][1000 genomes]
rs11953174	1.00[EUR][1000 genomes]
rs11954050	1.00[EUR][1000 genomes]
rs11954191	1.00[EUR][1000 genomes]
rs11954754	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11955985	1.00[EUR][1000 genomes]
rs11956324	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11957754	1.00[EUR][1000 genomes]
rs11959499	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16869036	1.00[EUR][1000 genomes]
rs16869039	1.00[EUR][1000 genomes]
rs16869046	1.00[EUR][1000 genomes]
rs16869069	1.00[EUR][1000 genomes]
rs16869072	1.00[EUR][1000 genomes]
rs16869075	1.00[EUR][1000 genomes]
rs16869076	1.00[EUR][1000 genomes]
rs16869091	1.00[EUR][1000 genomes]
rs2090594	1.00[EUR][1000 genomes]
rs41311331	1.00[EUR][1000 genomes]
rs57985920	1.00[EUR][1000 genomes]
rs62000408	1.00[EUR][1000 genomes]
rs6452897	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6452909	1.00[EUR][1000 genomes]
rs6861393	1.00[EUR][1000 genomes]
rs6868367	1.00[EUR][1000 genomes]
rs6868595	1.00[EUR][1000 genomes]
rs6879160	0.87[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6880756	1.00[EUR][1000 genomes]
rs6886689	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6891482	1.00[EUR][1000 genomes]
rs73179739	1.00[EUR][1000 genomes]
rs7706469	1.00[EUR][1000 genomes]
rs7706731	1.00[EUR][1000 genomes]
rs7716706	0.90[AMR][1000 genomes]
rs7718860	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7720923	1.00[EUR][1000 genomes]
rs7730198	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7732837	1.00[EUR][1000 genomes]
rs7733280	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432750	chr5:89410113-90137144	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv432751	chr5:89457044-90090444	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv529544	chr5:89523963-90412409	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv933668	chr5:89854253-89999672	Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
5	nsv531965	chr5:89886550-90145002	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:89892800-89909000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr5:89893000-89907800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr5:89893200-89902000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr5:89895000-89907400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr5:89899000-89900800	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr5:89899200-89900800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr5:89899200-89901000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr5:89899600-89902000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr5:89899800-89900800	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr5:89900000-89900800	Enhancers	Pancreatic Islets	Pancreatic Islet
11	chr5:89900200-89900800	Enhancers	Brain Anterior Caudate	brain
12	chr5:89900400-89901000	Enhancers	NH-A	brain
13	chr5:89900400-89903200	Enhancers	K562	blood
14	chr5:89900600-89900800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr5:89900600-89900800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr5:89900600-89900800	Bivalent Enhancer	A549	lung
17	chr5:89900600-89901000	Enhancers	Brain Angular Gyrus	brain
18	chr5:89900600-89901000	Enhancers	GM12878-XiMat	blood
19	chr5:89900600-89901000	Enhancers	Hela-S3	cervix
20	chr5:89900600-89901000	Enhancers	Osteobl	bone

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