Variant report

Variant	rs10061253
Chromosome Location	chr5:59042118-59042119
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	chr5:59022602..59025084-chr5:59040662..59042603,2	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1011644	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1370230	0.81[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap]
rs169869	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs17742664	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1992112	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2164661	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs256356	0.91[CHB][hapmap];0.88[JPT][hapmap]
rs2938784	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs2938785	0.91[CHB][hapmap];0.94[JPT][hapmap]
rs2963824	0.95[CHB][hapmap];0.87[JPT][hapmap]
rs298057	0.89[ASN][1000 genomes]
rs298058	0.95[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs298059	0.86[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs298061	0.95[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs298062	0.86[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs298063	0.86[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs298067	0.84[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs298072	0.81[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs298074	0.89[ASN][1000 genomes]
rs298075	0.91[ASN][1000 genomes]
rs298082	0.85[ASN][1000 genomes]
rs298083	0.91[ASN][1000 genomes]
rs298084	0.86[CHB][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs298091	0.86[CHB][hapmap];0.81[JPT][hapmap];0.88[ASN][1000 genomes]
rs298092	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs298093	0.95[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs298096	0.95[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs298097	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs402874	0.84[ASN][1000 genomes]
rs4235477	1.00[CHB][hapmap];0.87[JPT][hapmap];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6450526	0.86[CHB][hapmap];0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs6450527	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6450529	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6450531	0.91[CHB][hapmap];0.87[JPT][hapmap]
rs6450532	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs6865459	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6869459	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs6875753	0.91[CHB][hapmap];0.88[JPT][hapmap];0.96[ASN][1000 genomes]
rs7701573	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7701748	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs905834	0.95[CHB][hapmap];0.94[JPT][hapmap]

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	nsv881708	chr5:58869051-59093198	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1018015	chr5:58889470-59532667	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv537766	chr5:58889470-59532667	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv427720	chr5:58913581-59086987	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	11 gene(s)	inside rSNPs	diseases
5	nsv534614	chr5:58962510-59388525	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59028000-59043200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr5:59039400-59042600	Enhancers	HMEC	breast
3	chr5:59039400-59059800	Weak transcription	Primary B cells from cord blood	blood
4	chr5:59039600-59043000	Enhancers	HUVEC	blood vessel
5	chr5:59039800-59042600	Enhancers	Rectal Smooth Muscle	rectum
6	chr5:59039800-59042600	Enhancers	NH-A	brain
7	chr5:59040000-59042800	Enhancers	HSMM	muscle
8	chr5:59040200-59042600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr5:59040400-59043400	Enhancers	Colon Smooth Muscle	Colon
10	chr5:59040800-59042200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr5:59040800-59042200	Enhancers	Fetal Stomach	stomach
12	chr5:59041000-59042800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr5:59041000-59043400	Enhancers	Fetal Brain Male	brain
14	chr5:59041000-59047000	Weak transcription	Fetal Intestine Small	intestine
15	chr5:59041200-59042200	Enhancers	Osteobl	bone
16	chr5:59041200-59042600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr5:59041200-59042600	Enhancers	Fetal Muscle Leg	muscle
18	chr5:59041200-59042800	Enhancers	Muscle Satellite Cultured Cells	--
19	chr5:59041400-59042200	Weak transcription	NHDF-Ad	bronchial
20	chr5:59041400-59042400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr5:59041400-59042400	Weak transcription	Brain Cingulate Gyrus	brain
22	chr5:59041400-59042600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr5:59041400-59042600	Enhancers	Placenta Amnion	Placenta Amnion
24	chr5:59041600-59042200	Enhancers	Stomach Smooth Muscle	stomach
25	chr5:59041600-59042200	Enhancers	HSMMtube	muscle
26	chr5:59041600-59042600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr5:59041600-59042600	Enhancers	Brain Germinal Matrix	brain
28	chr5:59041600-59042600	Flanking Active TSS	Hela-S3	cervix
29	chr5:59041600-59043000	Enhancers	Fetal Lung	lung
30	chr5:59041600-59043000	Enhancers	NHEK	skin
31	chr5:59041600-59046400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr5:59041600-59049600	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr5:59041600-59052200	Weak transcription	Aorta	Aorta
34	chr5:59041800-59042200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr5:59041800-59043200	Flanking Active TSS	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links