Variant report

Variant	rs6548577
Chromosome Location	chr3:78567071-78567072
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:78565489..78567089-chr3:78577179..78578919,2	MCF-7	breast:

Extended variants
information (count: 61 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11709736	0.82[ASN][1000 genomes]
rs11713403	0.81[ASN][1000 genomes]
rs11721300	0.81[ASN][1000 genomes]
rs11916084	0.81[EUR][1000 genomes]
rs13079422	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13079826	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13098427	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1444482	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1444483	1.00[ASN][1000 genomes]
rs1596609	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1596610	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1822711	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1822712	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2028740	0.81[ASN][1000 genomes]
rs2120703	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2120704	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4302345	0.82[EUR][1000 genomes]
rs4342073	0.81[EUR][1000 genomes]
rs4555484	0.81[EUR][1000 genomes]
rs4680933	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4680990	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4680991	0.81[ASN][1000 genomes]
rs4680992	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4680993	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4680994	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4680995	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4680996	0.94[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs62256689	0.83[ASN][1000 genomes]
rs6548570	0.80[EUR][1000 genomes]
rs6548574	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6548575	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6548576	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6548578	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6548581	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6772687	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6793939	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6798454	0.80[EUR][1000 genomes]
rs6798540	0.80[EUR][1000 genomes]
rs6806585	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6808324	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs726722	0.83[ASN][1000 genomes]
rs7614720	0.81[EUR][1000 genomes]
rs7623401	0.81[EUR][1000 genomes]
rs9309805	0.81[EUR][1000 genomes]
rs9631522	0.93[AFR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9631523	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9809403	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9822941	0.81[EUR][1000 genomes]
rs9835912	0.81[EUR][1000 genomes]
rs9843660	0.81[EUR][1000 genomes]
rs9846994	0.81[ASN][1000 genomes]
rs9852892	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9857473	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9864442	0.83[ASN][1000 genomes]
rs991942	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877017	chr3:77881397-78670654	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv529995	chr3:78188643-78739698	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv1008156	chr3:78444137-78765884	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv834743	chr3:78494263-78663600	Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv1010650	chr3:78505564-78699161	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	esv1799120	chr3:78562104-78579242	Enhancers Weak transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:78566600-78567400	Enhancers	Brain Germinal Matrix	brain
2	chr3:78566800-78567600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr3:78566800-78568000	Enhancers	Fetal Lung	lung
4	chr3:78567000-78567400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:78567000-78567400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr3:78567000-78567400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr3:78567000-78567600	Enhancers	HepG2	liver

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