Variant report

Variant	rs60400559
Chromosome Location	chr2:98976342-98976343
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:98973452..98976374-chr7:75594519..75596340,2	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs12463618	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12464558	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12467200	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1546351	0.84[ASN][1000 genomes]
rs1546352	0.99[ASN][1000 genomes]
rs34118499	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3769755	0.88[ASN][1000 genomes]
rs4850873	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4851126	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4851127	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4851128	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55690937	0.94[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs55851325	0.99[ASN][1000 genomes]
rs55869498	0.94[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs56112202	0.94[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs56289599	0.93[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs56859980	0.93[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs57502811	0.93[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs57738681	0.94[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs58799739	0.94[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs59040049	0.94[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs59952489	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62156295	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62156307	0.94[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs62156315	0.93[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs62156316	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs6732568	0.93[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs6732654	0.93[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs6734225	0.90[EUR][1000 genomes]
rs72819945	0.93[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs867588	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs937727	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs937728	0.99[ASN][1000 genomes]
rs937729	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv518056	chr2:98586842-99156296	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1008645	chr2:98915767-99010743	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1010466	chr2:98938886-98998109	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1013617	chr2:98943377-99004173	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98976200-98976400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:98976200-98977000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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