Variant report

Variant	rs26561
Chromosome Location	chr5:111339403-111339404
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	chr5:111338145..111340158-chr5:111345203..111347809,2	MCF-7	breast:

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10059738	0.85[ASN][1000 genomes]
rs10063079	0.84[ASN][1000 genomes]
rs10463623	0.95[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs10463624	0.95[CHB][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs11241146	0.95[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs1493453	0.91[ASN][1000 genomes]
rs1494585	0.90[ASN][1000 genomes]
rs1507844	0.87[CEU][hapmap]
rs1540687	0.87[CEU][hapmap]
rs168875	0.82[ASN][1000 genomes]
rs2047070	0.90[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs2048155	0.85[CHB][hapmap];0.90[ASN][1000 genomes]
rs255910	0.88[ASN][1000 genomes]
rs255916	0.82[ASN][1000 genomes]
rs255920	0.81[ASN][1000 genomes]
rs255928	1.00[ASN][1000 genomes]
rs255929	0.96[ASN][1000 genomes]
rs255930	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs25790	0.87[CEU][hapmap];0.86[EUR][1000 genomes]
rs26539	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs26540	0.96[ASN][1000 genomes]
rs26541	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs26542	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs26543	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs26545	0.90[ASN][1000 genomes]
rs26546	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs26557	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs26558	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs26559	0.98[ASN][1000 genomes]
rs26560	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs26562	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs26563	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs27535	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34924	0.95[CHB][hapmap];0.90[JPT][hapmap];0.88[YRI][hapmap];0.94[ASN][1000 genomes]
rs34928	0.90[ASN][1000 genomes]
rs34930	0.90[ASN][1000 genomes]
rs34931	0.90[ASN][1000 genomes]
rs34941	0.95[ASN][1000 genomes]
rs34942	0.95[CHB][hapmap];0.85[JPT][hapmap];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35303575	0.91[ASN][1000 genomes]
rs35658682	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs36061964	0.86[ASN][1000 genomes]
rs36069145	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36133922	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs41142	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs42308	0.90[ASN][1000 genomes]
rs466033	0.95[CEU][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs474807	0.84[ASN][1000 genomes]
rs490821	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs490983	0.87[ASN][1000 genomes]
rs504582	0.85[ASN][1000 genomes]
rs508089	0.87[ASN][1000 genomes]
rs560063	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs593236	0.86[ASN][1000 genomes]
rs624694	0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs6881837	0.86[ASN][1000 genomes]
rs6882073	0.84[ASN][1000 genomes]
rs6882205	0.86[ASN][1000 genomes]
rs712660	0.87[ASN][1000 genomes]
rs7710690	0.95[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs7730997	0.88[ASN][1000 genomes]
rs7735316	0.87[ASN][1000 genomes]
rs9326846	0.91[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs980888	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	nsv599367	chr5:110924280-111602713	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv1015302	chr5:111339022-111802947	Enhancers Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv537861	chr5:111339022-111802947	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:111334800-111341000	Weak transcription	Psoas Muscle	Psoas
2	chr5:111335000-111340200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr5:111335000-111340200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr5:111335200-111340000	Weak transcription	HMEC	breast
5	chr5:111335200-111340200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr5:111335400-111340200	Weak transcription	HSMMtube	muscle
7	chr5:111335800-111339800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr5:111336000-111340000	Weak transcription	HSMM	muscle
9	chr5:111336000-111340200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr5:111336400-111339600	Weak transcription	Osteobl	bone
11	chr5:111337200-111342600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr5:111338000-111343000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr5:111338200-111340200	Weak transcription	NHEK	skin
14	chr5:111338400-111339800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr5:111338400-111340000	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr5:111338400-111340000	Weak transcription	NHLF	lung
17	chr5:111338400-111340200	Weak transcription	NH-A	brain
18	chr5:111338600-111340200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr5:111339000-111340200	Enhancers	NHDF-Ad	bronchial
20	chr5:111339400-111339600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr5:111339400-111339800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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