Variant report

Variant	rs49960
Chromosome Location	chr5:58012229-58012230
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1158196	0.81[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs12054892	0.80[JPT][hapmap]
rs12653046	0.85[JPT][hapmap]
rs149351	0.87[AFR][1000 genomes]
rs158986	0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs158988	0.91[CHB][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs158991	0.94[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs158992	0.91[CHB][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs158994	0.80[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs158995	0.94[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs158998	0.91[CHB][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs158999	0.95[LWK][hapmap];0.81[MKK][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes]
rs159001	0.90[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs159009	0.91[CHB][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs16877131	0.95[YRI][hapmap]
rs1833613	0.93[AFR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2591913	0.91[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs2591921	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2591923	0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2662624	0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs290572	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs290573	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs292994	0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs292995	0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs293004	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs293005	0.88[LWK][hapmap]
rs293016	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs293017	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs293019	0.89[YRI][hapmap];0.87[AFR][1000 genomes]
rs293021	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs293024	0.94[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs293028	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs293030	0.81[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.87[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs293031	0.81[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs58662773	0.87[AFR][1000 genomes]
rs6898044	0.80[JPT][hapmap]

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	nsv1029145	chr5:57905821-58141221	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv830311	chr5:57912546-58105636	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58001800-58013000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr5:58012000-58013200	Enhancers	iPS-18 Cell Line	embryonic stem cell
3	chr5:58012000-58013200	Enhancers	Liver	Liver
4	chr5:58012200-58014200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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