Variant report

Variant	rs17721564
Chromosome Location	chr5:58381186-58381187
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10065303	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10065699	0.83[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10076635	0.97[ASN][1000 genomes]
rs10452450	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12109774	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16889167	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16889175	0.86[JPT][hapmap]
rs17720871	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17721133	0.86[CEU][hapmap];0.81[AMR][1000 genomes]
rs17721311	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs17777280	0.88[CEU][hapmap];0.83[AMR][1000 genomes]
rs17777617	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs55801062	0.81[AMR][1000 genomes]
rs56407743	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62356680	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62356683	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62356684	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62356686	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62356687	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62356690	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62356691	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62356692	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62356694	0.83[EUR][1000 genomes]
rs6898082	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs950446	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.86[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	esv2830363	chr5:57893949-58555491	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv830312	chr5:58191579-58382226	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv830313	chr5:58273724-58421098	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58376400-58388200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr5:58376400-58389200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr5:58376400-58390400	Weak transcription	Hela-S3	cervix
4	chr5:58376600-58386200	Weak transcription	Colon Smooth Muscle	Colon
5	chr5:58376600-58387000	Weak transcription	Rectal Smooth Muscle	rectum
6	chr5:58376800-58385800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr5:58378200-58391800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr5:58380800-58383800	Enhancers	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links