Variant report

Variant	rs12488939
Chromosome Location	chr3:139050831-139050832
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:138662930..138665142-chr3:139048462..139050899,2	K562	blood:
2	chr3:139046649..139048613-chr3:139049792..139051458,2	MCF-7	breast:
3	chr3:138654402..138658110-chr3:139047575..139051045,3	K562	blood:

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1044826	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10460845	0.83[ASN][1000 genomes]
rs10935320	0.90[ASN][1000 genomes]
rs10935323	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12492883	0.84[AMR][1000 genomes]
rs12494806	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12695698	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12695699	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13060697	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13083195	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13085888	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13086868	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs13089007	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13089090	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13092507	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13092935	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1586861	0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1586863	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1586864	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17336869	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1907687	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2233811	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2233815	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2349059	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34623690	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3772877	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3772878	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3772879	0.81[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs3821544	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3821545	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4383548	0.87[AMR][1000 genomes]
rs4544576	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs67929453	0.86[ASN][1000 genomes]
rs6798217	0.87[AMR][1000 genomes]
rs7374385	0.80[EUR][1000 genomes]
rs9289576	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs9289578	1.00[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs964227	0.86[EUR][1000 genomes]
rs973691	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9812192	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9818691	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9825064	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9829163	0.84[AMR][1000 genomes]
rs9831108	1.00[CEU][hapmap];0.83[CHB][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9834607	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs9835241	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs9848241	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9849039	0.86[EUR][1000 genomes]
rs9849578	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9853350	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9860201	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9868544	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9882014	0.95[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.80[EUR][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	nsv1005158	chr3:139001736-139073011	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv877543	chr3:139021139-139327261	Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv4034	chr3:139034976-139080133	Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139048200-139062400	Weak transcription	Right Atrium	heart
2	chr3:139050600-139051400	Enhancers	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links