Variant report

Variant	rs1090293
Chromosome Location	chr20:22207156-22207157
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	chr20:22207148..22209709-chr20:22210226..22212970,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FOXA2-14	chr20:22205059-22209178	ucscGeneNc_uc002wsk_1

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1090292	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1159466	0.97[ASN][1000 genomes]
rs2876633	0.83[ASN][1000 genomes]
rs4815098	0.85[ASN][1000 genomes]
rs6082642	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6113583	0.84[ASN][1000 genomes]
rs6113585	0.85[ASN][1000 genomes]
rs6137582	0.83[ASN][1000 genomes]
rs709005	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs709006	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs709007	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs742655	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs804609	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs804610	0.85[ASN][1000 genomes]
rs804612	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs804614	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs804615	1.00[CEU][hapmap];0.89[CHB][hapmap];0.82[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs804616	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs804617	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs804618	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1058137	chr20:21549350-22295051	Weak transcription Bivalent Enhancer Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv1065067	chr20:22199617-22240462	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1090293	HSPC072	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:22206800-22207400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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