Variant report

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:64748389..64750742-chr14:64753810..64755799,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000140009	Chromatin interaction

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10143616	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs12101211	0.84[ASN][1000 genomes]
rs1256030	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs1256031	0.92[CEU][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs1256033	0.92[CEU][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs1256040	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs1256056	0.80[TSI][hapmap]
rs17101765	0.87[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs17179740	0.88[ASW][hapmap];0.87[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];0.83[LWK][hapmap];1.00[MKK][hapmap];0.87[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2978381	0.86[GIH][hapmap];0.80[JPT][hapmap]
rs2987983	0.83[GIH][hapmap]
rs3020444	0.87[CHB][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap]
rs3020445	0.81[CEU][hapmap];0.81[TSI][hapmap]
rs3020449	0.86[GIH][hapmap];0.80[JPT][hapmap]
rs3020450	0.81[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs3783736	0.86[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap];0.92[MKK][hapmap];0.84[ASN][1000 genomes]
rs6573552	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7154455	0.87[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap]
rs8011682	0.88[ASN][1000 genomes]
rs8020356	0.85[ASN][1000 genomes]
rs960070	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[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	nsv902019	chr14:64395569-64882380	Enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv456326	chr14:64420413-64754361	Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv564905	chr14:64420413-64754361	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv1307	chr14:64742037-64787315	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6573553	SYNE2	Cis_1M	lymphoblastoid	RTeQTL
rs6573553	ESR2	Cis_1M	lymphoblastoid	RTeQTL
rs6573553	SYNE2	cis	multi-tissue	Pritchard
rs6573553	ESR2	cis	Skin Sun Exposed Lower leg	GTEx
rs6573553	MTHFD1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:64727600-64757600	Weak transcription	Ovary	ovary
2	chr14:64735400-64757200	Weak transcription	Thymus	Thymus
3	chr14:64749600-64756400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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