Variant report

Variant	rs10489395
Chromosome Location	chr1:186467429-186467430
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	chr1:186462234..186463900-chr1:186466419..186468938,2	MCF-7	breast:

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10158395	0.90[YRI][hapmap]
rs10489394	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10494585	0.91[YRI][hapmap];1.00[AMR][1000 genomes]
rs10494588	0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs12239085	0.87[AMR][1000 genomes]
rs12239322	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs12239327	0.87[AMR][1000 genomes]
rs13374147	0.87[AMR][1000 genomes]
rs13374242	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13375943	0.90[YRI][hapmap]
rs13376114	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13376658	0.87[AMR][1000 genomes]
rs16825179	0.91[YRI][hapmap]
rs16825187	0.88[YRI][hapmap];0.89[AMR][1000 genomes]
rs16825277	0.90[YRI][hapmap];0.89[AMR][1000 genomes]
rs16825282	0.90[YRI][hapmap];0.89[AMR][1000 genomes]
rs16825292	0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs16825329	0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs16825448	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16825457	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1929094	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3934201	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs41393449	0.97[AFR][1000 genomes]
rs56158125	0.87[AMR][1000 genomes]
rs56888492	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57020506	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs57488115	0.87[AMR][1000 genomes]
rs58300321	0.87[AMR][1000 genomes]
rs58336827	0.87[AMR][1000 genomes]
rs58410196	0.87[AMR][1000 genomes]
rs59886878	0.83[AFR][1000 genomes]
rs60957652	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6425029	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6673816	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6679283	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs6688055	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6695920	0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs7355201	0.87[AMR][1000 genomes]
rs7355203	1.00[AMR][1000 genomes]
rs7530502	0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7547924	0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs9803910	0.87[AMR][1000 genomes]

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	nsv1004481	chr1:186095854-186750968	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv535223	chr1:186095854-186750968	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	nsv1012164	chr1:186323867-186565995	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	esv2762201	chr1:186323879-186566007	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv832059	chr1:186464932-186639125	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:186452200-186467800	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr1:186452400-186468400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr1:186459400-186471800	Weak transcription	Brain Angular Gyrus	brain
4	chr1:186462600-186469600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr1:186462800-186467600	Weak transcription	Hela-S3	cervix
6	chr1:186462800-186468000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr1:186464200-186469600	Weak transcription	Aorta	Aorta
8	chr1:186464800-186467600	Weak transcription	HMEC	breast
9	chr1:186465000-186467800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr1:186465400-186467600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:186465400-186467600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:186465400-186468000	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr1:186465400-186468600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr1:186466000-186467600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr1:186466400-186471000	Weak transcription	Brain Anterior Caudate	brain
16	chr1:186466600-186470600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr1:186467000-186471000	Weak transcription	GM12878-XiMat	blood
18	chr1:186467000-186471400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr1:186467200-186468000	Flanking Active TSS	A549	lung
20	chr1:186467200-186468800	Enhancers	NH-A	brain
21	chr1:186467200-186470200	Enhancers	HUVEC	blood vessel
22	chr1:186467200-186471200	Weak transcription	Brain Cingulate Gyrus	brain
23	chr1:186467200-186474400	Enhancers	NHDF-Ad	bronchial
24	chr1:186467400-186469000	Enhancers	Stomach Mucosa	stomach
25	chr1:186467400-186469400	Enhancers	Osteobl	bone
26	chr1:186467400-186470600	Enhancers	NHEK	skin

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