Variant report

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:118994260..118996031-chr3:119041098..119043621,2	MCF-7	breast:
2	chr3:118994969..118996823-chr3:119062476..119065328,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000241155	Chromatin interaction

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

rs_ID	r²[population]
rs10511385	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11918598	0.85[CEU][hapmap]
rs11918661	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11922580	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12637189	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12639418	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17281577	0.92[CEU][hapmap];0.82[MEX][hapmap]
rs55642684	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56007616	0.93[EUR][1000 genomes]
rs56054255	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56176656	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56355928	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56397530	1.00[ASN][1000 genomes]
rs724653	0.85[CEU][hapmap]
rs7646428	0.93[ASN][1000 genomes]
rs9813454	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9828634	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9839704	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9856953	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9884021	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	esv18354	chr3:118855337-119000251	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16829649	PARVB	trans	cerebellum	SCAN
rs16829649	CD86	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:118994200-118995800	Enhancers	Primary T cells from cord blood	blood
2	chr3:118994400-118995600	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr3:118994400-118995600	Enhancers	Fetal Thymus	thymus
4	chr3:118994400-118995600	Enhancers	Thymus	Thymus
5	chr3:118994400-118995800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:118994400-118995800	Enhancers	Left Ventricle	heart
7	chr3:118994400-118996400	Enhancers	Lung	lung
8	chr3:118994600-118996400	Enhancers	Placenta	Placenta
9	chr3:118994800-118995400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr3:118994800-118997800	Weak transcription	Fetal Heart	heart
11	chr3:118994800-118998000	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr3:118994800-118998000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr3:118995000-118997000	Weak transcription	Right Atrium	heart
14	chr3:118995000-118997800	Weak transcription	A549	lung
15	chr3:118995200-118997600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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