Variant report

Variant	rs3891858
Chromosome Location	chr9:12716172-12716173
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	chr9:12715023..12717622-chr9:12718396..12720573,2	MCF-7	breast:

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1063380	0.81[LWK][hapmap]
rs10960766	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10960767	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10960768	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11787674	0.95[EUR][1000 genomes]
rs11787999	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs11788192	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11789339	0.88[EUR][1000 genomes]
rs11789481	0.83[EUR][1000 genomes]
rs11789805	0.88[EUR][1000 genomes]
rs11791497	0.93[EUR][1000 genomes]
rs11791954	0.95[EUR][1000 genomes]
rs11793178	0.88[EUR][1000 genomes]
rs11793280	0.85[CEU][hapmap]
rs11794050	0.95[EUR][1000 genomes]
rs11794202	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12001299	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12001737	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12001745	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12001885	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12001964	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12005881	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16929383	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16929385	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16929391	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16929400	1.00[CEU][hapmap];0.81[MKK][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16929473	0.85[CEU][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs17280279	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs17280629	0.98[EUR][1000 genomes]
rs17346748	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2209278	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs2733833	0.80[LWK][hapmap]
rs34509359	0.98[EUR][1000 genomes]
rs35238630	0.88[EUR][1000 genomes]
rs35852762	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35866166	0.98[EUR][1000 genomes]
rs41306290	0.98[EUR][1000 genomes]
rs61758391	0.95[EUR][1000 genomes]
rs61758394	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62638049	0.95[EUR][1000 genomes]
rs7025241	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7025758	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7026121	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7026199	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7030751	0.90[EUR][1000 genomes]
rs7033962	0.90[EUR][1000 genomes]
rs7035710	0.86[EUR][1000 genomes]
rs7040346	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7041590	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7041735	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73402088	0.81[EUR][1000 genomes]
rs73402092	0.81[EUR][1000 genomes]
rs768617	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7875424	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7876041	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2759671	chr9:12235048-12784092	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv1034393	chr9:12278703-12798236	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv869288	chr9:12286919-12816766	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv498136	chr9:12387840-12984158	Genic enhancers Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv1029415	chr9:12424340-12794623	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv540064	chr9:12424340-12794623	Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	esv2422212	chr9:12448789-13127738	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv1016570	chr9:12576095-12722387	Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	esv2758182	chr9:12621991-12784092	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv613613	chr9:12641987-12773263	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:12709200-12718400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr9:12711200-12722400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr9:12716000-12716200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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