Variant report

Variant	rs9296830
Chromosome Location	chr6:56021135-56021136
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: 122 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs1012257	0.89[ASN][1000 genomes]
rs1022539	0.84[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1033478	0.84[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs12190324	0.93[ASN][1000 genomes]
rs12199712	0.81[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs12199742	0.84[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.93[ASN][1000 genomes]
rs1319111	0.80[CEU][hapmap];0.84[CHB][hapmap];0.93[ASN][1000 genomes]
rs1319112	0.84[JPT][hapmap]
rs13193925	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13209836	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1480	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs1555097	0.81[CEU][hapmap];0.82[CHB][hapmap];0.84[JPT][hapmap]
rs1925138	0.91[ASN][1000 genomes]
rs1925139	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1925141	0.84[JPT][hapmap]
rs1925143	0.84[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs1925144	0.93[ASN][1000 genomes]
rs1925147	0.84[JPT][hapmap]
rs1925149	0.83[CHB][hapmap];0.83[ASN][1000 genomes]
rs1925179	1.00[CHB][hapmap];0.92[JPT][hapmap];0.99[ASN][1000 genomes]
rs1925180	0.97[ASN][1000 genomes]
rs1925181	0.88[CHB][hapmap];0.84[JPT][hapmap];0.99[ASN][1000 genomes]
rs1925185	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1925186	0.99[ASN][1000 genomes]
rs1925189	0.84[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1980487	0.84[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2038149	0.92[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2038150	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs2206674	0.80[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap]
rs2328675	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2328677	0.81[CHB][hapmap];0.99[ASN][1000 genomes]
rs2397204	1.00[CHB][hapmap];0.93[JPT][hapmap];0.99[ASN][1000 genomes]
rs2397206	0.90[ASN][1000 genomes]
rs2397208	0.87[CEU][hapmap];0.92[CHB][hapmap];0.84[JPT][hapmap];0.93[ASN][1000 genomes]
rs2745366	0.81[CEU][hapmap];0.82[CHB][hapmap];0.84[JPT][hapmap]
rs2745369	0.91[ASN][1000 genomes]
rs2764046	0.83[CEU][hapmap];0.90[CHB][hapmap]
rs2764052	0.80[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs2764055	0.87[ASN][1000 genomes]
rs2764056	0.87[ASN][1000 genomes]
rs2764059	0.84[ASN][1000 genomes]
rs2840995	0.91[ASN][1000 genomes]
rs2841000	0.92[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs2841006	0.81[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs2841007	0.80[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs2876630	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3817983	0.81[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs3846918	0.81[CEU][hapmap];0.82[CHB][hapmap];0.84[JPT][hapmap]
rs3846920	0.81[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs3846921	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs3846922	0.84[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.93[ASN][1000 genomes]
rs3846923	0.84[CEU][hapmap];0.81[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs3846924	0.84[CEU][hapmap];0.83[CHB][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs3846925	0.90[ASN][1000 genomes]
rs3857611	0.84[JPT][hapmap]
rs3857612	0.81[CEU][hapmap];0.82[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs3996940	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs4119567	0.84[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4126555	0.93[ASN][1000 genomes]
rs4126556	0.93[ASN][1000 genomes]
rs4126557	0.93[ASN][1000 genomes]
rs4126558	0.84[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs4140573	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4379279	0.80[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs4490668	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4495274	0.84[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4554321	0.90[ASN][1000 genomes]
rs4573075	0.80[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs4596475	0.81[CEU][hapmap];0.82[CHB][hapmap];0.84[JPT][hapmap]
rs4599643	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs4607420	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4712113	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4715585	0.92[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4715588	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4715589	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4715591	0.92[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs4715592	0.91[ASN][1000 genomes]
rs4715593	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4715597	0.84[JPT][hapmap]
rs6459124	0.82[ASN][1000 genomes]
rs6459128	0.88[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6459129	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6459133	0.84[CEU][hapmap];0.92[CHB][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6459134	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6459136	0.84[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6904431	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6904899	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6908195	0.93[ASN][1000 genomes]
rs6909268	0.90[JPT][hapmap]
rs6911907	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6914495	0.84[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.93[ASN][1000 genomes]
rs6914892	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6917593	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6922057	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6927919	0.81[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap]
rs6933151	0.92[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6934945	0.87[ASN][1000 genomes]
rs6935152	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6935200	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6939465	0.92[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs6939632	0.91[ASN][1000 genomes]
rs7450147	0.93[ASN][1000 genomes]
rs7754787	0.90[ASN][1000 genomes]
rs7762422	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7774374	0.84[CHB][hapmap];0.93[JPT][hapmap];0.97[ASN][1000 genomes]
rs9296828	0.81[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs9357891	1.00[CHB][hapmap];0.93[JPT][hapmap];0.99[ASN][1000 genomes]
rs9357892	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9357894	0.80[ASN][1000 genomes]
rs9370485	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9370486	0.92[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9382583	0.81[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap]
rs9382595	0.84[CEU][hapmap];0.83[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs9396176	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9396181	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9464348	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9475593	0.92[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9475621	0.84[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs994667	0.80[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.99[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:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:55984000-56037000	Weak transcription	Fetal Kidney	kidney
2	chr6:55999000-56021200	Weak transcription	Aorta	Aorta
3	chr6:56013000-56036400	Weak transcription	Colon Smooth Muscle	Colon
4	chr6:56019400-56023400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr6:56019600-56021800	Strong transcription	Fetal Muscle Leg	muscle
6	chr6:56019800-56021800	Strong transcription	Fetal Muscle Trunk	muscle
7	chr6:56020000-56021800	Strong transcription	Fetal Lung	lung
8	chr6:56020000-56023400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr6:56020200-56021800	Enhancers	HepG2	liver
10	chr6:56020400-56026000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr6:56020600-56021800	Strong transcription	Ovary	ovary
12	chr6:56021000-56021600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr6:56021000-56021600	Strong transcription	Stomach Smooth Muscle	stomach
14	chr6:56021000-56021800	Enhancers	Fetal Stomach	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links