Variant report

Variant	rs12490659
Chromosome Location	chr3:89184635-89184636
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:89179300..89181545-chr3:89184054..89185924,2	MCF-7	breast:

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

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

rs_ID	r²[population]
rs1040015	0.89[ASN][1000 genomes]
rs11914680	1.00[CEU][hapmap]
rs11914760	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11916891	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11918311	1.00[CEU][hapmap]
rs11919574	1.00[CEU][hapmap]
rs11921042	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs11928901	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12486049	1.00[CEU][hapmap]
rs12487141	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12490373	0.91[EUR][1000 genomes]
rs12491480	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12493524	0.92[EUR][1000 genomes]
rs12493527	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12494615	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12495783	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12496609	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12496791	0.89[ASN][1000 genomes]
rs13058761	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13058886	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13060198	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13071923	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13074291	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs13075931	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs13084503	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13089469	1.00[CEU][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13095092	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13097212	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13097548	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13098003	0.93[CEU][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13101118	1.00[CEU][hapmap]
rs1512909	0.93[CEU][hapmap]
rs34493897	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34638812	0.91[EUR][1000 genomes]
rs34855223	0.89[ASN][1000 genomes]
rs34893903	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34992749	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35053334	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35156943	0.89[ASN][1000 genomes]
rs35445148	1.00[CEU][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35971332	0.89[ASN][1000 genomes]
rs4132274	1.00[CEU][hapmap]
rs56408441	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56938121	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59668913	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6778523	0.81[AMR][1000 genomes]
rs71322851	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71322854	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71322855	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71322856	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71322857	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs71322858	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7430987	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7432443	1.00[CEU][hapmap]
rs7631932	0.93[CEU][hapmap]
rs7635321	0.87[CEU][hapmap]
rs7637578	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs7638207	1.00[CEU][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7642606	1.00[CEU][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[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	nsv877159	chr3:89018866-89207222	Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv998460	chr3:89064073-89188335	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv536638	chr3:89064073-89188335	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	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
5	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

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:89174000-89193200	Weak transcription	Fetal Brain Female	brain
2	chr3:89176800-89184800	Weak transcription	Fetal Muscle Leg	muscle
3	chr3:89177600-89187200	Weak transcription	Fetal Lung	lung
4	chr3:89179600-89188000	Weak transcription	Stomach Smooth Muscle	stomach
5	chr3:89183000-89187000	Weak transcription	Fetal Stomach	stomach
6	chr3:89184200-89185000	Weak transcription	Brain Germinal Matrix	brain
7	chr3:89184600-89190600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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