Variant report

Variant	rs13193002
Chromosome Location	chr6:54600704-54600705
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:54600004..54603656-chr6:54710742..54713977,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168143	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1039693	0.81[CEU][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs10447377	1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs10948842	0.95[ASN][1000 genomes]
rs11757171	1.00[CHB][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs11964037	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12211545	0.95[ASN][1000 genomes]
rs12215844	0.85[ASN][1000 genomes]
rs13200833	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13217514	0.82[CEU][hapmap];0.82[JPT][hapmap]
rs1359009	0.82[ASN][1000 genomes]
rs1911508	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2089411	0.93[ASN][1000 genomes]
rs2174145	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs2174735	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2297804	0.82[CEU][hapmap];0.82[JPT][hapmap]
rs6459021	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6899853	0.82[CEU][hapmap];0.82[JPT][hapmap]
rs6908136	0.98[ASN][1000 genomes]
rs6914808	0.81[ASN][1000 genomes]
rs6916681	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs6918290	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6929108	0.81[ASN][1000 genomes]
rs72967406	0.84[EUR][1000 genomes]
rs925057	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9464114	0.82[ASN][1000 genomes]
rs9464116	0.89[ASN][1000 genomes]
rs9464135	0.84[EUR][1000 genomes]
rs9474940	0.82[ASN][1000 genomes]
rs9474943	0.82[ASN][1000 genomes]
rs9474944	0.85[ASN][1000 genomes]
rs9474965	0.97[ASN][1000 genomes]
rs9474972	0.81[CEU][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs9474973	0.88[CHB][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9474977	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9474987	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9474991	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs981682	0.82[CEU][hapmap];0.82[JPT][hapmap]
rs9885668	0.95[ASN][1000 genomes]
rs995951	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[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	nsv885900	chr6:54517968-54852462	Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv885901	chr6:54588069-54635417	Enhancers Weak transcription Strong transcription Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv885902	chr6:54588069-54656673	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54600200-54612400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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