Variant report

No.	Distal block	Cell Line	Cell type
1	chr3:54375027..54375990-chr3:54387842..54389644,8	MCF-7	breast:
2	chr3:54375174..54375975-chr3:54461350..54461870,2	MCF-7	breast:
3	chr3:54375117..54375902-chr3:54387751..54388811,4	MCF-7	breast:
4	chr3:54375152..54375990-chr3:54394183..54395021,3	MCF-7	breast:
5	chr3:54375381..54375990-chr3:54394183..54394906,2	MCF-7	breast:
6	chr3:54375027..54375647-chr3:54388254..54389644,4	MCF-7	breast:

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11130416	0.88[ASW][hapmap];1.00[CEU][hapmap];0.86[CHD][hapmap];0.93[TSI][hapmap];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11130417	1.00[CEU][hapmap];0.82[CHB][hapmap];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4928040	1.00[CEU][hapmap];0.86[CHD][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6445645	0.94[EUR][1000 genomes]
rs6445648	1.00[CEU][hapmap];0.86[CHD][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6784315	1.00[CEU][hapmap];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6810202	0.83[AFR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7427630	0.92[EUR][1000 genomes]
rs7429094	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs7431577	1.00[CEU][hapmap];0.84[TSI][hapmap];0.94[EUR][1000 genomes]
rs7434239	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7618315	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7627905	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs7632823	0.88[GIH][hapmap];0.84[TSI][hapmap]
rs7634811	0.83[AFR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7652209	1.00[CEU][hapmap];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9818348	0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs9849660	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs9863855	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs9879885	1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.84[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	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1014595	chr3:53944473-54846754	Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv817328	chr3:54250314-54380438	Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv817210	chr3:54365684-54511164	Enhancers Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9683195	CCDC66	cis	parietal	SCAN
rs9683195	TUSC2	cis	cerebellum	SCAN
rs9683195	TEX264	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54368000-54378200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:54370600-54378200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:54373000-54376400	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr3:54375600-54380000	Weak transcription	Spleen	Spleen
5	chr3:54375600-54382000	Weak transcription	Hela-S3	cervix

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