Variant report

Variant	rs6879405
Chromosome Location	chr5:52486476-52486477
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10513015	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1374055	0.97[ASN][1000 genomes]
rs1374059	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1500363	0.89[ASN][1000 genomes]
rs1500364	0.89[ASN][1000 genomes]
rs1500365	0.89[ASN][1000 genomes]
rs1500366	0.89[ASN][1000 genomes]
rs1500367	0.89[ASN][1000 genomes]
rs1500368	0.89[ASN][1000 genomes]
rs1500369	0.89[ASN][1000 genomes]
rs153681	0.89[ASN][1000 genomes]
rs153684	0.89[ASN][1000 genomes]
rs16881049	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16881068	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1814735	0.89[ASN][1000 genomes]
rs1846702	0.89[ASN][1000 genomes]
rs1846703	0.89[ASN][1000 genomes]
rs254474	0.89[ASN][1000 genomes]
rs254520	0.89[ASN][1000 genomes]
rs254521	0.89[ASN][1000 genomes]
rs254625	0.89[ASN][1000 genomes]
rs254632	0.89[ASN][1000 genomes]
rs254633	0.89[ASN][1000 genomes]
rs2547522	0.89[ASN][1000 genomes]
rs2561392	0.89[ASN][1000 genomes]
rs2591905	0.89[ASN][1000 genomes]
rs2591906	0.89[ASN][1000 genomes]
rs2591907	0.89[ASN][1000 genomes]
rs2650677	0.89[ASN][1000 genomes]
rs2650680	0.89[ASN][1000 genomes]
rs2650681	0.89[ASN][1000 genomes]
rs2650682	0.89[ASN][1000 genomes]
rs2650683	0.89[ASN][1000 genomes]
rs2937663	0.89[ASN][1000 genomes]
rs6450114	1.00[ASN][1000 genomes]
rs6450118	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6450119	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6872198	0.94[ASN][1000 genomes]
rs6883958	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6892025	0.89[ASN][1000 genomes]
rs6895567	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs726904	0.89[ASN][1000 genomes]
rs726905	0.89[ASN][1000 genomes]
rs73100427	1.00[ASN][1000 genomes]
rs7703368	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7714660	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7723126	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs937579	0.89[ASN][1000 genomes]
rs937580	0.86[ASN][1000 genomes]
rs937582	0.83[ASN][1000 genomes]
rs9918234	0.84[AFR][1000 genomes];0.83[AMR][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	nsv949005	chr5:52188028-52808229	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	esv2752745	chr5:52422063-53343529	Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52486000-52488200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:52486400-52487000	Enhancers	HepG2	liver
3	chr5:52486400-52491000	Enhancers	Hela-S3	cervix

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