Variant report

Variant	rs1925179
Chromosome Location	chr6:56021212-56021213
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	chr6:56020919..56023138-chr6:56026048..56027819,2	MCF-7	breast:

Extended variants
information (count: 129 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:126)

rs_ID	r²[population]
rs1012257	0.90[ASN][1000 genomes]
rs1022539	0.92[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1033478	0.84[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1205109	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12190324	0.91[ASN][1000 genomes]
rs12199712	0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12199742	0.92[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1319111	0.84[CHB][hapmap];0.89[CHD][hapmap];0.80[JPT][hapmap];0.91[ASN][1000 genomes]
rs1319112	0.81[CEU][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap]
rs13193925	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs13209836	0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1480	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs1555097	1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1925138	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1925139	0.91[ASN][1000 genomes]
rs1925141	0.82[CEU][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap]
rs1925143	0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1925144	0.91[ASN][1000 genomes]
rs1925147	0.82[CEU][hapmap];0.92[JPT][hapmap]
rs1925149	0.82[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs1925177	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1925180	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1925181	0.88[CHB][hapmap];0.83[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1925185	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1925186	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1925189	0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1980487	0.92[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2038149	0.92[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2206674	1.00[CEU][hapmap];0.92[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs2328675	0.94[ASN][1000 genomes]
rs2328677	0.95[CEU][hapmap];0.81[CHB][hapmap];0.94[CHD][hapmap];0.85[JPT][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2397204	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2397206	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2397208	0.92[CHB][hapmap];0.83[CHD][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs2397209	0.81[ASN][1000 genomes]
rs2745366	1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2745369	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2764046	1.00[CEU][hapmap];0.90[CHB][hapmap]
rs2764048	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2764050	0.83[EUR][1000 genomes]
rs2764052	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2764055	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2764056	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2764059	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2840989	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2840990	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2840995	0.93[ASN][1000 genomes]
rs2841000	0.82[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2841006	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2841007	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2876630	0.91[ASN][1000 genomes]
rs3817983	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3846918	1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3846920	1.00[CEU][hapmap];0.84[CHB][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3846921	0.95[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3846922	0.92[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3846923	0.81[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3846924	0.83[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3846925	0.89[ASN][1000 genomes]
rs3857611	0.82[CEU][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap]
rs3857612	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3996940	0.91[CEU][hapmap];0.82[CHB][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4119567	0.92[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4126555	0.91[ASN][1000 genomes]
rs4126556	0.91[ASN][1000 genomes]
rs4126557	0.91[ASN][1000 genomes]
rs4126558	0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4140573	0.91[ASN][1000 genomes]
rs4379279	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4490668	0.94[ASN][1000 genomes]
rs4495274	0.92[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4554321	0.89[ASN][1000 genomes]
rs4573075	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4596475	1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap]
rs4599643	0.95[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs4607420	0.99[ASN][1000 genomes]
rs4712113	0.91[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4715585	0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4715588	0.94[ASN][1000 genomes]
rs4715589	0.91[ASN][1000 genomes]
rs4715591	0.87[ASW][hapmap];0.82[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4715592	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4715593	0.91[ASN][1000 genomes]
rs4715597	0.82[CEU][hapmap];0.92[JPT][hapmap]
rs6459124	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6459127	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6459128	0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6459129	0.94[ASN][1000 genomes]
rs6459133	0.92[CHB][hapmap];0.87[CHD][hapmap];0.80[JPT][hapmap];0.94[ASN][1000 genomes]
rs6459134	0.94[ASN][1000 genomes]
rs6459136	0.92[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6904431	0.91[ASN][1000 genomes]
rs6904899	0.91[ASN][1000 genomes]
rs6908195	0.91[ASN][1000 genomes]
rs6909268	0.90[CEU][hapmap];0.81[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6911907	0.91[ASN][1000 genomes]
rs6914495	0.92[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6914892	0.91[ASN][1000 genomes]
rs6917593	0.99[ASN][1000 genomes]
rs6922057	0.99[ASN][1000 genomes]
rs6927919	1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6933151	0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6934945	0.86[ASN][1000 genomes]
rs6935152	0.91[ASN][1000 genomes]
rs6935200	0.91[ASN][1000 genomes]
rs6939465	0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6939632	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7450147	0.91[ASN][1000 genomes]
rs7754787	0.89[ASN][1000 genomes]
rs7762422	0.90[ASN][1000 genomes]
rs7774374	0.86[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9296828	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9296830	1.00[CHB][hapmap];0.92[JPT][hapmap];0.99[ASN][1000 genomes]
rs9357891	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9357892	0.96[ASN][1000 genomes]
rs9370485	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9370486	0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9382583	1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9382595	0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9396176	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9396181	0.91[ASN][1000 genomes]
rs9464348	0.97[ASN][1000 genomes]
rs9475560	0.84[AMR][1000 genomes]
rs9475593	0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9475621	0.92[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs994667	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][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	nsv1034037	chr6:55222409-56069600	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv885911	chr6:55789704-56143231	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv526703	chr6:55810482-56023811	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:55984000-56037000	Weak transcription	Fetal Kidney	kidney
2	chr6:56013000-56036400	Weak transcription	Colon Smooth Muscle	Colon
3	chr6:56019400-56023400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr6:56019600-56021800	Strong transcription	Fetal Muscle Leg	muscle
5	chr6:56019800-56021800	Strong transcription	Fetal Muscle Trunk	muscle
6	chr6:56020000-56021800	Strong transcription	Fetal Lung	lung
7	chr6:56020000-56023400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr6:56020200-56021800	Enhancers	HepG2	liver
9	chr6:56020400-56026000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr6:56020600-56021800	Strong transcription	Ovary	ovary
11	chr6:56021000-56021600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr6:56021000-56021600	Strong transcription	Stomach Smooth Muscle	stomach
13	chr6:56021000-56021800	Enhancers	Fetal Stomach	stomach
14	chr6:56021200-56021600	Enhancers	NH-A	brain
15	chr6:56021200-56021800	Strong transcription	Aorta	Aorta

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