Variant report

Variant	rs12494615
Chromosome Location	chr3:89264399-89264400
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1040015	0.83[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];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11916891	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11918311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs11919574	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs11921042	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs11928901	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12486049	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12487141	0.85[ASN][1000 genomes]
rs12490659	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12491480	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12493527	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12495783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12496279	0.86[EUR][1000 genomes]
rs12496609	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12496791	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13058761	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13058886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13060198	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13070668	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13071923	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13074291	1.00[CEU][hapmap]
rs13075931	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs13084503	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13089469	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13093815	0.95[YRI][hapmap]
rs13095092	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13097212	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13097548	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13098003	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13101118	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1512909	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs34493897	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34855223	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34893903	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34992749	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35053334	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35156943	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35445148	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35971332	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4132274	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs56408441	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56938121	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59668913	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6778523	0.84[EUR][1000 genomes]
rs71322851	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71322854	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71322855	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71322856	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71322857	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71322858	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7430987	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7432443	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs7631932	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs7635321	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs7637578	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[YRI][hapmap]
rs7638207	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7642606	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.92[ASN][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	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	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
3	nsv437866	chr3:89247881-89480265	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
4	esv2757001	chr3:89260495-89271087	Weak transcription Enhancers Active TSS Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
5	esv2759160	chr3:89260495-89271087	Weak transcription Flanking Active TSS Enhancers Active TSS	n/a	n/a	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:89259800-89266200	Weak transcription	Fetal Muscle Leg	muscle
2	chr3:89259800-89266600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr3:89260400-89265800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr3:89262400-89265800	Weak transcription	Rectal Smooth Muscle	rectum
5	chr3:89263600-89265600	Weak transcription	Fetal Stomach	stomach
6	chr3:89263600-89265800	Weak transcription	Fetal Brain Female	brain
7	chr3:89263600-89277000	Weak transcription	Brain Germinal Matrix	brain
8	chr3:89264000-89264800	Weak transcription	Fetal Brain Male	brain
9	chr3:89264000-89265200	Weak transcription	Fetal Lung	lung

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