Variant report

Variant	rs1609688
Chromosome Location	chr3:160877096-160877097
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:160876047..160878704-chr3:160883637..160886578,2	MCF-7	breast:

Extended variants
information (count: 124 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:123)

rs_ID	r²[population]
rs1026572	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs1037888	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10513562	0.86[CEU][hapmap]
rs10804790	0.82[AMR][1000 genomes]
rs10936223	0.91[EUR][1000 genomes]
rs1154701	1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs12493960	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12631850	0.91[EUR][1000 genomes]
rs13066683	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13098884	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1382427	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs1382428	0.80[AMR][1000 genomes]
rs1478565	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs1599374	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1599376	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1599378	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1599379	0.82[EUR][1000 genomes]
rs1599381	0.85[EUR][1000 genomes]
rs1599383	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1599386	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1599389	0.85[EUR][1000 genomes]
rs1599390	0.85[EUR][1000 genomes]
rs1600209	0.82[AMR][1000 genomes]
rs1610158	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs163327	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs163328	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs189270	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes]
rs1993891	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs2306061	0.93[CEU][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2404340	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2593812	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs28515190	0.82[AMR][1000 genomes]
rs336541	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs336543	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs336548	0.82[AMR][1000 genomes]
rs336567	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs336570	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs336577	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs336593	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs339101	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3849524	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4273380	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4342141	0.85[CEU][hapmap]
rs4370045	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4414866	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4493449	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4518145	0.88[AMR][1000 genomes]
rs4557202	0.93[CEU][hapmap];0.85[EUR][1000 genomes]
rs4597724	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4616689	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4618258	0.93[CEU][hapmap];0.84[EUR][1000 genomes]
rs4679926	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4856739	0.88[AMR][1000 genomes]
rs5004752	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6441354	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs6441370	0.83[AMR][1000 genomes]
rs6441371	0.83[AMR][1000 genomes]
rs6441373	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6762645	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6765269	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6765270	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6769642	0.93[ASN][1000 genomes]
rs6774276	1.00[JPT][hapmap];0.88[AMR][1000 genomes]
rs6774635	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6775627	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6778254	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6783085	0.85[EUR][1000 genomes]
rs6789244	0.85[EUR][1000 genomes]
rs6789388	1.00[JPT][hapmap];0.88[AMR][1000 genomes]
rs6794601	0.82[CEU][hapmap]
rs6799130	0.84[EUR][1000 genomes]
rs6806054	0.86[CEU][hapmap]
rs7611367	1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs7614375	0.85[EUR][1000 genomes]
rs7615592	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7617204	0.85[EUR][1000 genomes]
rs7619011	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7622047	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7623206	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7625363	0.84[EUR][1000 genomes]
rs7629987	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7630674	0.82[CEU][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7630768	0.85[EUR][1000 genomes]
rs7632423	0.85[CEU][hapmap]
rs7632797	1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs7633186	1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs7633857	0.85[EUR][1000 genomes]
rs7637086	0.85[EUR][1000 genomes]
rs7638668	0.82[AMR][1000 genomes]
rs7647285	0.85[EUR][1000 genomes]
rs7647327	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7650703	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7651087	0.85[EUR][1000 genomes]
rs7653361	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs778642	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs778643	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs778645	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs778646	0.86[ASN][1000 genomes]
rs778649	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs778653	0.85[CEU][hapmap]
rs778654	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs778657	0.86[CEU][hapmap]
rs796609	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs898680	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs898681	0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs9290065	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9290069	0.88[CEU][hapmap];0.88[EUR][1000 genomes]
rs9290074	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs975323	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs980975	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs980976	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9811594	0.85[CEU][hapmap]
rs9820825	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9821201	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes]
rs9831488	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9846756	0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9847866	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9848239	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9860360	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9867582	0.82[EUR][1000 genomes]
rs9870059	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9875200	0.86[CEU][hapmap]
rs9879687	0.81[EUR][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	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 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	chr3:160850400-160882400	Weak transcription	Ovary	ovary
2	chr3:160862200-160882400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:160867400-160877800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr3:160867600-160880800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:160876200-160880600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr3:160876800-160877200	Enhancers	HMEC	breast

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