Variant report

Variant	rs162870
Chromosome Location	chr3:78877217-78877218
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:78875620..78878075-chr3:78879470..78882248,2	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11127634	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12495127	0.83[AMR][1000 genomes]
rs13087237	0.83[AMR][1000 genomes]
rs1480687	0.88[CEU][hapmap]
rs1480688	0.88[CEU][hapmap];0.81[TSI][hapmap]
rs1487139	1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs1840969	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs1843786	0.84[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.95[ASN][1000 genomes]
rs28629289	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs333491	0.80[CHD][hapmap];1.00[JPT][hapmap]
rs333495	1.00[JPT][hapmap]
rs416551	0.83[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs439325	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs444598	0.89[CHB][hapmap]
rs510006	0.89[CHB][hapmap];0.84[CHD][hapmap];0.84[JPT][hapmap]
rs6762005	0.84[JPT][hapmap]
rs9309818	0.85[AMR][1000 genomes]
rs9309819	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.88[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9309820	0.88[CEU][hapmap]
rs9631512	0.85[AMR][1000 genomes]
rs9835958	0.92[CEU][hapmap];0.87[TSI][hapmap]
rs9837982	0.88[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9861264	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9863758	0.84[CEU][hapmap]
rs9873248	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9877603	0.84[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9881587	0.88[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010804	chr3:78739648-79087470	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv533681	chr3:78750924-79017336	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv877019	chr3:78808850-78877217	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:78851400-78880400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:78868000-78881600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:78873200-78879600	Weak transcription	Brain Substantia Nigra	brain
4	chr3:78873200-78888800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:78873800-78881800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr3:78875000-78880600	Weak transcription	HepG2	liver
7	chr3:78875600-78884400	Weak transcription	NHDF-Ad	bronchial
8	chr3:78875600-78888800	Weak transcription	Fetal Lung	lung
9	chr3:78876200-78881600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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