Variant report

Variant	rs59000628
Chromosome Location	chr5:124799006-124799007
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:124797532..124799322-chr5:124800167..124802283,2	MCF-7	breast:

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1554281	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55717300	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56707415	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56821497	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56835569	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56988571	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57118683	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57123863	1.00[AMR][1000 genomes]
rs57697012	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58308815	1.00[AMR][1000 genomes]
rs58338793	1.00[AMR][1000 genomes]
rs58631543	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58917396	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59380738	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59958060	1.00[EUR][1000 genomes]
rs60202964	1.00[EUR][1000 genomes]
rs60214755	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61304237	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61472360	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6595615	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6870489	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6878929	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6883449	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6883628	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6884059	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6884354	1.00[AMR][1000 genomes]
rs6890153	1.00[AMR][1000 genomes]
rs6894842	1.00[AMR][1000 genomes]
rs73303332	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73303334	1.00[AMR][1000 genomes]
rs73303374	1.00[AMR][1000 genomes]
rs73303384	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73303399	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73303400	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73305305	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73305308	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73305320	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73305337	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73305339	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73305342	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73305345	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73305365	1.00[EUR][1000 genomes]
rs73305368	1.00[EUR][1000 genomes]
rs73305401	1.00[EUR][1000 genomes]
rs73307316	1.00[EUR][1000 genomes]
rs73312635	1.00[EUR][1000 genomes]
rs7702589	1.00[AMR][1000 genomes]
rs7711951	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7725952	1.00[AMR][1000 genomes]
rs7729702	1.00[AMR][1000 genomes]
rs7729817	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7730376	1.00[AMR][1000 genomes]
rs7730445	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7732317	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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	nsv1030992	chr5:124708549-125391503	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv537892	chr5:124708549-125391503	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv882824	chr5:124789500-124875058	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:124797800-124799200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr5:124797800-124800600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr5:124798000-124799200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr5:124798600-124800000	Enhancers	Brain Germinal Matrix	brain
5	chr5:124798800-124799400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr5:124798800-124799800	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr5:124799000-124800000	Enhancers	Fetal Brain Female	brain

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