Variant report

Variant	rs2039879
Chromosome Location	chr9:79371761-79371762
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:79370786..79371842-chr9:79602290..79603157,3	MCF-7	breast:
2	chr9:79370999..79371885-chr9:79602318..79602838,2	MCF-7	breast:
3	chr9:79370822..79371805-chr9:79602182..79602729,2	K562	blood:

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10217198	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12337262	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12555311	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12684201	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1343401	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1343407	0.82[ASN][1000 genomes]
rs17787305	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61401332	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7038114	0.82[ASN][1000 genomes]
rs73460219	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73460240	0.89[ASN][1000 genomes]
rs73460246	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9314856	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869152	chr9:78742197-79583399	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1040363	chr9:79246366-79711737	Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	esv2758190	chr9:79365865-79673907	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	esv2759697	chr9:79365865-79673907	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 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	chr9:79361200-79396600	Weak transcription	Aorta	Aorta
2	chr9:79364400-79372000	Weak transcription	Brain Hippocampus Middle	brain
3	chr9:79364600-79387000	Weak transcription	Brain Cingulate Gyrus	brain
4	chr9:79364800-79373600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr9:79364800-79374800	Weak transcription	Colon Smooth Muscle	Colon
6	chr9:79370200-79372800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr9:79370200-79375800	Enhancers	Primary B cells from cord blood	blood
8	chr9:79370400-79372800	Enhancers	Brain Germinal Matrix	brain
9	chr9:79370600-79376600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr9:79370800-79376800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr9:79371000-79371800	Weak transcription	Stomach Smooth Muscle	stomach
12	chr9:79371000-79376400	Enhancers	Primary B cells from peripheral blood	blood
13	chr9:79371200-79372400	Enhancers	Brain Substantia Nigra	brain
14	chr9:79371200-79373400	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr9:79371400-79372400	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr9:79371400-79372600	Enhancers	Fetal Brain Male	brain
17	chr9:79371600-79372800	Enhancers	GM12878-XiMat	blood
18	chr9:79371600-79374000	Weak transcription	HSMM	muscle
19	chr9:79371600-79376800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr9:79371600-79400200	Weak transcription	HSMMtube	muscle

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