Variant report

Variant	rs12258938
Chromosome Location	chr10:92609876-92609877
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: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10881829	0.87[ASN][1000 genomes]
rs10881831	0.94[ASN][1000 genomes]
rs10881833	0.95[ASN][1000 genomes]
rs10881834	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10881835	0.95[ASN][1000 genomes]
rs10881841	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10881843	0.94[ASN][1000 genomes]
rs10881845	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10881846	0.94[ASN][1000 genomes]
rs10881848	0.94[ASN][1000 genomes]
rs10881850	0.92[ASN][1000 genomes]
rs11186282	0.84[ASN][1000 genomes]
rs11186292	0.87[ASN][1000 genomes]
rs11186298	0.90[ASN][1000 genomes]
rs11186299	0.90[ASN][1000 genomes]
rs11186305	0.94[ASN][1000 genomes]
rs11186306	0.95[ASN][1000 genomes]
rs11186315	0.93[ASN][1000 genomes]
rs11186323	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11186333	1.00[ASN][1000 genomes]
rs11186336	0.95[ASN][1000 genomes]
rs11186338	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11186339	0.87[ASN][1000 genomes]
rs11186343	0.98[ASN][1000 genomes]
rs11186344	0.98[ASN][1000 genomes]
rs11186346	0.98[ASN][1000 genomes]
rs11186352	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11186358	0.92[ASN][1000 genomes]
rs11186359	0.92[ASN][1000 genomes]
rs11186360	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11186361	0.92[ASN][1000 genomes]
rs11186367	0.92[ASN][1000 genomes]
rs11186368	0.95[ASN][1000 genomes]
rs11498506	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11498507	0.95[ASN][1000 genomes]
rs11498662	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11527868	0.95[ASN][1000 genomes]
rs12220866	0.90[ASN][1000 genomes]
rs12244538	0.96[ASN][1000 genomes]
rs12249377	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12255018	0.94[ASN][1000 genomes]
rs12256605	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12261011	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12264160	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1573253	0.87[ASN][1000 genomes]
rs1592143	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17102362	0.92[ASN][1000 genomes]
rs1891311	0.98[ASN][1000 genomes]
rs1891312	0.94[ASN][1000 genomes]
rs2901026	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2901127	0.98[ASN][1000 genomes]
rs4144422	0.94[ASN][1000 genomes]
rs4282910	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4284320	0.87[ASN][1000 genomes]
rs4586057	0.94[ASN][1000 genomes]
rs58578719	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59257274	0.84[ASN][1000 genomes]
rs61481895	0.94[ASN][1000 genomes]
rs7082814	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7085559	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7096568	0.94[ASN][1000 genomes]
rs73315609	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73315628	1.00[ASN][1000 genomes]
rs74148885	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7478556	0.84[ASN][1000 genomes]
rs7903584	0.92[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	chr10:92605600-92610000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr10:92607400-92610200	Enhancers	HMEC	breast
4	chr10:92609200-92610200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr10:92609200-92610200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr10:92609200-92610200	Enhancers	HSMM	muscle
7	chr10:92609200-92610200	Flanking Active TSS	NHEK	skin
8	chr10:92609400-92610200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr10:92609400-92610400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
10	chr10:92609600-92610000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr10:92609600-92610200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr10:92609600-92610200	Enhancers	HSMMtube	muscle
13	chr10:92609600-92610200	Enhancers	Osteobl	bone
14	chr10:92609600-92610600	Enhancers	NH-A	brain
15	chr10:92609600-92610800	Enhancers	Muscle Satellite Cultured Cells	--

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