Variant report

Variant	rs10489394
Chromosome Location	chr1:186456892-186456893
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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]
rs10489395	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	nsv527758	chr1:186452071-186456977	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 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	chr1:186453200-186461400	Weak transcription	HUVEC	blood vessel
4	chr1:186453200-186461600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:186455200-186457000	Enhancers	A549	lung
6	chr1:186456000-186457400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:186456000-186461800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr1:186456200-186457000	Enhancers	NHDF-Ad	bronchial
9	chr1:186456400-186457200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr1:186456400-186459400	Weak transcription	NHEK	skin
11	chr1:186456400-186461600	Weak transcription	Hela-S3	cervix
12	chr1:186456800-186461400	Weak transcription	Osteobl	bone

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