Variant report

Variant	rs12109253
Chromosome Location	chr5:89909722-89909723
allele	A/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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr5:89908527..89910983-chr5:89912943..89914483,2	K562	blood:
2	chr5:89908957..89911258-chr5:89952267..89954603,2	K562	blood:
3	chr5:89908105..89911531-chr5:89917925..89920470,3	K562	blood:
4	chr5:89903854..89914063-chr5:89934543..89943749,18	K562	blood:
5	chr5:89908130..89913352-chr5:89914891..89917115,4	K562	blood:
6	chr5:89705226..89707879-chr5:89908779..89911338,2	K562	blood:
7	chr5:89904971..89912478-chr5:89936195..89941599,10	K562	blood:
8	chr5:89908142..89911258-chr5:89951635..89955571,4	K562	blood:
9	chr5:89908014..89912492-chr5:89923558..89929663,6	K562	blood:
10	chr5:89881845..89884640-chr5:89908883..89910553,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000153140	Chromatin interaction
ENSG00000164199	Chromatin interaction
ENSG00000255647	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs12108970	1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1504986	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1504997	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16868834	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16868842	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16868848	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16868851	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16868853	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16868854	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41304890	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56926055	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61740119	1.00[AMR][1000 genomes]
rs73179766	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73179768	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73179771	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73179774	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73179777	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73179793	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73181603	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73181604	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73181609	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73181619	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73181634	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73181640	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73181642	1.00[AMR][1000 genomes]
rs73181647	1.00[AMR][1000 genomes]
rs73181653	1.00[AMR][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:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:89902600-89917400	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr5:89907400-89911000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr5:89907800-89909800	Enhancers	H9 Cell Line	embryonic stem cell
4	chr5:89907800-89910200	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr5:89908200-89910200	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr5:89908200-89910600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr5:89908400-89909800	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr5:89908400-89910000	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr5:89908600-89909800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
10	chr5:89908600-89909800	Flanking Active TSS	GM12878-XiMat	blood
11	chr5:89909000-89909800	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr5:89909000-89910000	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr5:89909200-89909800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr5:89909200-89911800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr5:89909400-89909800	Flanking Active TSS	Fetal Brain Female	brain
16	chr5:89909400-89909800	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr5:89909400-89910000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
18	chr5:89909600-89909800	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr5:89909600-89909800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr5:89909600-89909800	Active TSS	Brain Germinal Matrix	brain
21	chr5:89909600-89909800	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr5:89909600-89909800	Active TSS	K562	blood
23	chr5:89909600-89910000	Enhancers	NH-A	brain
24	chr5:89909600-89911200	Weak transcription	HUES64 Cell Line	embryonic stem cell

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