Variant report

Variant	rs12339502
Chromosome Location	chr9:16063841-16063842
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:16063712..16066364-chr9:16092575..16094646,2	MCF-7	breast:

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10119089	0.88[EUR][1000 genomes]
rs10511612	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10962269	0.81[ASN][1000 genomes]
rs12003062	0.86[ASN][1000 genomes]
rs13347415	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17784173	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28422784	0.84[ASN][1000 genomes]
rs2987094	0.86[AMR][1000 genomes]
rs4961637	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4961643	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9886829	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv892625	chr9:15326251-16064850	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv949463	chr9:15970668-16377360	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv831521	chr9:15974174-16106565	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1025555	chr9:16022186-16064158	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	esv2761506	chr9:16040491-16093736	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv525782	chr9:16061960-16071439	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
7	esv2757319	chr9:16063191-16082467	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
8	esv2759672	chr9:16063191-16082467	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
9	esv2756177	chr9:16063191-16082467	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16048600-16071400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr9:16058600-16065200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr9:16058600-16069400	Weak transcription	Fetal Lung	lung
4	chr9:16058600-16069600	Weak transcription	NHLF	lung
5	chr9:16058800-16066000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr9:16060800-16065000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr9:16060800-16065600	Enhancers	HMEC	breast
8	chr9:16061200-16064000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr9:16062200-16065000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr9:16062200-16065000	Enhancers	NH-A	brain
11	chr9:16062400-16064200	Enhancers	Hela-S3	cervix
12	chr9:16062600-16064200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr9:16063400-16064600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr9:16063400-16064600	Enhancers	NHEK	skin
15	chr9:16063400-16065600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr9:16063600-16064000	Enhancers	A549	lung
17	chr9:16063600-16064200	Enhancers	Muscle Satellite Cultured Cells	--
18	chr9:16063600-16064600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr9:16063800-16064600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr9:16063800-16069000	Weak transcription	Osteobl	bone
21	chr9:16063800-16069200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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