Variant report

Variant	rs12259062
Chromosome Location	chr10:92610045-92610046
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	chr10:92605355..92608309-chr10:92609468..92612446,2	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10785972	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10881838	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10881839	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10881844	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11186320	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11186324	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11186350	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11186351	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11597471	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11599902	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12246757	0.88[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12254390	0.88[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12259060	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12259401	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs35987367	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4520504	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4522081	0.88[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4568910	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4933618	0.88[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6583737	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66650915	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7080463	0.93[ASN][1000 genomes]
rs7082401	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7087400	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7089472	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7101301	0.87[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7896973	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7900048	0.87[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7905446	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7906960	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7909232	0.87[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[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	nsv948363	chr10:92084520-92614402	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv831945	chr10:92590576-92793582	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:92597800-92616200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr10:92607400-92610200	Enhancers	HMEC	breast
3	chr10:92609200-92610200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr10:92609200-92610200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr10:92609200-92610200	Enhancers	HSMM	muscle
6	chr10:92609200-92610200	Flanking Active TSS	NHEK	skin
7	chr10:92609400-92610200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr10:92609400-92610400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
9	chr10:92609600-92610200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr10:92609600-92610200	Enhancers	HSMMtube	muscle
11	chr10:92609600-92610200	Enhancers	Osteobl	bone
12	chr10:92609600-92610600	Enhancers	NH-A	brain
13	chr10:92609600-92610800	Enhancers	Muscle Satellite Cultured Cells	--
14	chr10:92610000-92610200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr10:92610000-92610800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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