Variant report

Variant	rs9866580
Chromosome Location	chr3:180165224-180165225
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1353679	0.84[EUR][1000 genomes]
rs1532485	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs1603658	0.84[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs17707963	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17708913	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17764356	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28385473	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28495789	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62291004	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62291005	0.92[EUR][1000 genomes]
rs62291006	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62291007	0.89[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs62291008	0.92[EUR][1000 genomes]
rs62291009	0.92[EUR][1000 genomes]
rs62291043	0.84[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs62291045	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs62291048	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6770664	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs6774942	0.84[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs7626274	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9290705	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9819839	1.00[EUR][1000 genomes]
rs9832227	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9837678	0.84[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs9846858	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9847201	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9857489	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs9858483	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs9864401	0.88[AMR][1000 genomes]
rs9864959	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9865590	0.80[YRI][hapmap]
rs9872076	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9876153	0.84[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9877497	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012271	chr3:179806875-180234871	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv997388	chr3:179899279-180172349	Enhancers Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv536817	chr3:179899279-180172349	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1007831	chr3:180162003-180348203	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv536818	chr3:180162003-180348203	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:180164000-180165400	Enhancers	HMEC	breast
2	chr3:180164400-180165800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr3:180164400-180166200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr3:180164800-180165800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr3:180165000-180171400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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