Variant report

Variant	rs13089469
Chromosome Location	chr3:89211879-89211880
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1040015	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11914680	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11914760	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11916891	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11918311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11919574	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs11921042	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11928901	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12486049	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs12487141	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12490373	0.82[EUR][1000 genomes]
rs12490659	1.00[CEU][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12491480	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12493524	0.83[EUR][1000 genomes]
rs12493527	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12494615	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12495783	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12496609	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12496791	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13058761	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13058886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs13060198	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13071923	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13074291	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs13075931	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13084503	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13095092	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13097212	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13097548	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13098003	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13101118	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs1512909	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs34493897	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34638812	0.82[EUR][1000 genomes]
rs34855223	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34893903	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34992749	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35053334	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35156943	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35445148	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35971332	0.89[ASN][1000 genomes]
rs4132274	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs56408441	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56938121	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59668913	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6778523	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs71322851	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71322854	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71322855	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71322856	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71322857	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71322858	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7430987	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7432443	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7631932	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7635321	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7637578	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs7638207	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7642606	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834760	chr3:89085529-89299398	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1005603	chr3:89174152-89223459	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv997874	chr3:89188275-89279573	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1008916	chr3:89206065-89241915	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:89210400-89212200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr3:89211400-89212200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:89211600-89212000	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr3:89211600-89212200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:89211600-89212200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:89211600-89217400	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr3:89211800-89212200	Enhancers	H1 Cell Line	embryonic stem cell
8	chr3:89211800-89212200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr3:89211800-89213400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr3:89211800-89213600	Weak transcription	iPS-20b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links