Variant report

Variant	rs12003808
Chromosome Location	chr9:22228560-22228561
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:21813976..21815531-chr9:22227768..22230145,2	MCF-7	breast:

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11788928	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11790978	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs11792798	0.90[EUR][1000 genomes]
rs11792897	1.00[CEU][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11792932	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs16905769	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2025797	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2383209	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2383212	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2383213	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs4461984	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4540492	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4621906	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4644346	0.95[EUR][1000 genomes]
rs62555449	0.85[EUR][1000 genomes]
rs62555450	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62555451	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62555452	0.95[EUR][1000 genomes]
rs62555453	0.90[EUR][1000 genomes]
rs62555455	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62559460	0.95[EUR][1000 genomes]
rs62559467	0.95[EUR][1000 genomes]
rs62559468	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62559469	0.95[EUR][1000 genomes]
rs62559470	0.95[EUR][1000 genomes]
rs62559471	0.95[EUR][1000 genomes]
rs62559472	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62559473	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62559474	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62559475	0.95[EUR][1000 genomes]
rs62559493	0.87[EUR][1000 genomes]
rs62559494	0.82[EUR][1000 genomes]
rs62559495	0.82[EUR][1000 genomes]
rs6475620	0.90[EUR][1000 genomes]
rs7035115	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs73442947	0.90[EUR][1000 genomes]
rs73444955	0.95[EUR][1000 genomes]
rs736723	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs7848967	0.90[EUR][1000 genomes]
rs7853527	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs7853566	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7859353	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7859407	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs7872728	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs943399	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[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	nsv529609	chr9:21708371-22537069	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv531617	chr9:21985057-22809676	Genic enhancers Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv892749	chr9:22125913-22244280	Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv1021264	chr9:22159622-22293804	Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv1033789	chr9:22183150-22266091	Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1029289	chr9:22193167-23023688	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv1016067	chr9:22210874-22432654	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv1015364	chr9:22211364-22416886	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv540086	chr9:22211364-22416886	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:22219600-22230600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr9:22226600-22229000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr9:22227400-22228800	Weak transcription	A549	lung
4	chr9:22228400-22229200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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