Variant report

Variant	rs3116601
Chromosome Location	chr13:51108096-51108097
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	chr13:50760566..50762913-chr13:51108077..51110898,2	MCF-7	breast:

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1262870	1.00[AFR][1000 genomes]
rs1327646	0.81[AMR][1000 genomes]
rs1341637	0.84[EUR][1000 genomes]
rs157164	0.80[EUR][1000 genomes]
rs157165	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1630605	0.80[EUR][1000 genomes]
rs1638703	0.80[EUR][1000 genomes]
rs1753633	0.80[EUR][1000 genomes]
rs1753639	0.80[EUR][1000 genomes]
rs183950	0.80[EUR][1000 genomes]
rs201754	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs201755	0.83[ASN][1000 genomes]
rs201757	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs201762	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs202346	0.81[EUR][1000 genomes]
rs2225226	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2408045	0.86[EUR][1000 genomes]
rs3116598	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3116599	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3116600	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3116602	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3116603	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3116604	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3116605	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3116606	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3116607	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3116613	0.86[EUR][1000 genomes]
rs3116615	0.86[EUR][1000 genomes]
rs3116616	0.85[EUR][1000 genomes]
rs3116617	0.86[EUR][1000 genomes]
rs3118903	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3118905	1.00[ASN][1000 genomes]
rs3118906	1.00[ASN][1000 genomes]
rs3118909	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3118910	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3118912	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3118913	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3118914	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3118915	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3118918	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3118919	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3118920	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs495838	0.80[EUR][1000 genomes]
rs7337757	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[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	nsv1035151	chr13:50513535-51167850	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1254 gene(s)	inside rSNPs	diseases
2	esv2753964	chr13:50545399-51421199	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
3	esv2753492	chr13:50550081-51461720	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 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	chr13:51103800-51110600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr13:51104800-51108400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr13:51104800-51110600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr13:51106200-51108400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr13:51106200-51110600	Weak transcription	HSMM	muscle
6	chr13:51107000-51110200	Weak transcription	HUVEC	blood vessel
7	chr13:51107200-51110400	Weak transcription	NH-A	brain
8	chr13:51107400-51110400	Weak transcription	Thymus	Thymus
9	chr13:51107800-51109600	ZNF genes & repeats	Dnd41	blood

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