Variant report

Variant	rs42546
Chromosome Location	chr5:4977036-4977037
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10038746	0.96[EUR][1000 genomes]
rs10038747	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10058490	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1035914	0.97[EUR][1000 genomes]
rs1452027	0.97[EUR][1000 genomes]
rs168733	0.83[CEU][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs181822	0.80[CEU][hapmap];0.81[EUR][1000 genomes]
rs189835	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1901498	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2399756	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs249457	0.81[EUR][1000 genomes]
rs249458	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs249459	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2561719	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2561720	0.96[CEU][hapmap];0.97[EUR][1000 genomes]
rs2561721	0.96[CEU][hapmap];0.97[EUR][1000 genomes]
rs2561722	0.97[EUR][1000 genomes]
rs2600655	0.88[EUR][1000 genomes]
rs30449	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs30450	0.80[CEU][hapmap];0.81[EUR][1000 genomes]
rs30451	0.83[CEU][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs30462	0.81[EUR][1000 genomes]
rs30463	0.83[EUR][1000 genomes]
rs30464	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs30465	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs30466	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs30468	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs30469	0.86[EUR][1000 genomes]
rs30470	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs30471	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs30472	0.82[EUR][1000 genomes]
rs30473	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs30474	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs30475	0.96[EUR][1000 genomes]
rs374207	0.88[EUR][1000 genomes]
rs39586	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs39849	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs39850	0.83[EUR][1000 genomes]
rs39851	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs39852	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs39853	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs40468	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs42400	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs42401	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs42545	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60185285	0.82[EUR][1000 genomes]
rs719183	0.86[EUR][1000 genomes]
rs9313095	0.96[CEU][hapmap];0.97[EUR][1000 genomes]
rs935857	0.96[CEU][hapmap];0.97[EUR][1000 genomes]
rs935858	0.97[EUR][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	nsv1019579	chr5:4557477-4997411	Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1021653	chr5:4932992-5201887	Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1028717	chr5:4954566-4993583	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:4976200-4978400	Enhancers	Cortex derived primary cultured neurospheres	brain
2	chr5:4976400-4977200	Enhancers	Fetal Kidney	kidney
3	chr5:4976600-4977200	Enhancers	Ovary	ovary
4	chr5:4976600-4977400	Enhancers	Fetal Muscle Leg	muscle
5	chr5:4976600-4978200	Enhancers	NH-A	brain
6	chr5:4976800-4977200	Enhancers	Fetal Lung	lung
7	chr5:4976800-4978400	Enhancers	Osteobl	bone
8	chr5:4977000-4977200	Enhancers	Brain Angular Gyrus	brain
9	chr5:4977000-4977200	Enhancers	Brain Substantia Nigra	brain
10	chr5:4977000-4977600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr5:4977000-4977800	Weak transcription	Pancreas	Pancrea

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