Variant report

Variant	rs12490953
Chromosome Location	chr3:54817204-54817205
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	chr3:54812123..54813966-chr3:54816428..54818136,2	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10510773	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12488046	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12490327	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs12496821	0.89[CHB][hapmap]
rs13068008	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13070262	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13083683	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13084602	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs13086256	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13088416	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs13090131	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13092066	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13095178	0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs13100029	0.83[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs1344671	0.84[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1520575	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs17815840	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs1882320	0.93[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1882322	0.84[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1921548	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2099019	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs3852006	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3864001	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3868872	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs3906509	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4025824	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4083342	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs6808464	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs6809269	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6809715	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7618235	0.84[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7618991	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7623961	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs7636321	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014595	chr3:53944473-54846754	Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54807600-54836000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr3:54815600-54823800	Weak transcription	Aorta	Aorta
3	chr3:54815800-54817600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr3:54815800-54828400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr3:54816000-54817800	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr3:54816000-54826000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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