Variant report

Variant	rs58500396
Chromosome Location	chr9:8802404-8802405
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs12348514	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12555236	0.88[EUR][1000 genomes]
rs1836233	0.90[ASN][1000 genomes]
rs60584517	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62528842	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62530574	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022796	chr9:8360729-9110046	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv892235	chr9:8700396-8865925	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1025800	chr9:8712487-9030627	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv539980	chr9:8712487-9030627	Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv892236	chr9:8745520-8870553	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1015898	chr9:8753534-9011443	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv892239	chr9:8773599-8805462	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region	1 gene(s)	inside rSNPs	diseases
8	nsv892240	chr9:8796449-8834108	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:8794200-8821800	Weak transcription	Primary hematopoietic stem cells	blood
2	chr9:8794800-8825600	Weak transcription	Ovary	ovary
3	chr9:8798400-8815400	Weak transcription	Fetal Brain Male	brain
4	chr9:8799200-8809000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr9:8799400-8806400	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr9:8799600-8806400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr9:8799800-8806200	Weak transcription	Brain Substantia Nigra	brain
8	chr9:8800000-8807800	Weak transcription	Brain Cingulate Gyrus	brain
9	chr9:8800000-8809000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr9:8800600-8806600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr9:8800600-8810800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr9:8800800-8804400	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr9:8800800-8807600	Weak transcription	Brain Angular Gyrus	brain
14	chr9:8800800-8808800	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr9:8800800-8809800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr9:8801800-8803000	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr9:8802000-8802600	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr9:8802000-8802600	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr9:8802000-8802600	Enhancers	Stomach Mucosa	stomach
20	chr9:8802200-8802600	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr9:8802200-8802600	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr9:8802200-8802600	Enhancers	iPS-18 Cell Line	embryonic stem cell
23	chr9:8802200-8802600	Enhancers	Duodenum Mucosa	Duodenum
24	chr9:8802200-8802800	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr9:8802400-8802600	Enhancers	iPS-20b Cell Line	embryonic stem cell
26	chr9:8802400-8802600	Genic enhancers	Fetal Lung	lung
27	chr9:8802400-8802600	Enhancers	Placenta Amnion	Placenta Amnion
28	chr9:8802400-8802600	Active TSS	Rectal Mucosa Donor 29	rectum
29	chr9:8802400-8802800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr9:8802400-8803000	Genic enhancers	Brain Hippocampus Middle	brain

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