Variant report

Variant	rs898415
Chromosome Location	chr3:53667639-53667640
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	chr3:53661729..53666678-chr3:53666737..53670217,5	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1037827	0.91[EUR][1000 genomes]
rs11130373	0.82[EUR][1000 genomes]
rs1380606	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1380609	0.88[MKK][hapmap]
rs1401494	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1599230	0.81[CEU][hapmap];0.81[TSI][hapmap]
rs1599231	1.00[YRI][hapmap]
rs1841291	0.88[CEU][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2250736	0.85[CEU][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.97[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2612022	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2633707	0.89[CEU][hapmap];0.90[GIH][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2633731	0.92[CHB][hapmap]
rs2680654	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2680656	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3774472	1.00[YRI][hapmap]
rs3774481	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs3774486	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3774491	0.82[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];0.80[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6445590	0.90[CEU][hapmap];0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs6445591	0.92[EUR][1000 genomes]
rs6786135	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6809164	0.92[CHB][hapmap]
rs754063	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7630805	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap]
rs898416	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs930949	0.90[EUR][1000 genomes]
rs9846874	0.81[CEU][hapmap]
rs9850569	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs9883910	0.95[AMR][1000 genomes];0.97[EUR][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	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	nsv1001128	chr3:53659570-53927842	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53652800-53684000	Weak transcription	Right Atrium	heart
2	chr3:53664000-53668600	Weak transcription	Gastric	stomach
3	chr3:53666400-53668200	Enhancers	Stomach Mucosa	stomach
4	chr3:53666400-53681400	Weak transcription	Fetal Lung	lung
5	chr3:53667000-53667800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr3:53667600-53667800	Enhancers	Liver	Liver
7	chr3:53667600-53668000	Enhancers	Fetal Intestine Small	intestine
8	chr3:53667600-53668600	Enhancers	HepG2	liver
9	chr3:53667600-53680600	Weak transcription	Fetal Intestine Large	intestine

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