Variant report

Variant	rs12594677
Chromosome Location	chr15:59994943-59994944
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:59992550..59995081-chr15:59995698..59998010,2	MCF-7	breast:

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10152209	0.94[YRI][hapmap]
rs10152373	1.00[CEU][hapmap];0.84[JPT][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10152414	0.94[YRI][hapmap]
rs10152415	0.95[YRI][hapmap]
rs10152431	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10152791	1.00[CEU][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1046053	0.95[YRI][hapmap]
rs10519039	0.81[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13379702	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13380147	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1552031	0.95[YRI][hapmap]
rs16941645	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16941648	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17236804	0.95[YRI][hapmap]
rs1871500	0.95[YRI][hapmap]
rs2306355	0.95[YRI][hapmap]
rs2306357	1.00[YRI][hapmap]
rs2307275	0.95[YRI][hapmap]
rs3087328	0.91[LWK][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap]
rs3894007	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4232	0.86[YRI][hapmap]
rs4774340	0.95[YRI][hapmap]
rs4775195	0.95[YRI][hapmap]
rs4775197	0.90[YRI][hapmap]
rs56141740	0.83[AFR][1000 genomes]
rs58190651	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6151446	1.00[YRI][hapmap]
rs6151447	1.00[YRI][hapmap]
rs6151448	1.00[YRI][hapmap]
rs6151449	1.00[YRI][hapmap]
rs6151450	1.00[YRI][hapmap]
rs6151458	0.95[YRI][hapmap]
rs6151461	0.95[YRI][hapmap]
rs6151462	0.95[YRI][hapmap]
rs6151496	0.95[YRI][hapmap]
rs6151504	0.95[YRI][hapmap]
rs6151529	0.89[YRI][hapmap]
rs6151532	0.88[YRI][hapmap]
rs6151533	0.90[YRI][hapmap]
rs6151535	0.91[YRI][hapmap]
rs6151536	0.90[YRI][hapmap]
rs6151571	0.89[YRI][hapmap]
rs6151588	0.82[YRI][hapmap]
rs6494131	0.95[YRI][hapmap]
rs7162964	0.95[YRI][hapmap]
rs7180408	0.95[YRI][hapmap]
rs7182962	0.94[YRI][hapmap]
rs72625734	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72625735	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72625736	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs74017838	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8025415	0.87[ASW][hapmap];1.00[CEU][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8026680	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8027353	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8027389	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8027415	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][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	nsv527307	chr15:59103328-60018487	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
2	nsv533240	chr15:59858093-59998176	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv526682	chr15:59992758-59994943	Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59989800-59995000	Enhancers	NHEK	skin
2	chr15:59989800-59998400	Enhancers	Hela-S3	cervix
3	chr15:59992800-59996800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr15:59993000-59998000	Weak transcription	HMEC	breast
5	chr15:59993600-59995800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr15:59994400-59996600	Enhancers	A549	lung
7	chr15:59994400-59997800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr15:59994600-59996000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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