Variant report

Variant	rs724677
Chromosome Location	chr6:56120721-56120722
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	chr6:56120518..56123285-chr6:56126655..56128230,2	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10456731	1.00[CEU][hapmap]
rs12195053	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12209054	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12209474	0.89[ASN][1000 genomes]
rs12213867	0.89[ASN][1000 genomes]
rs3846930	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3996938	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4361616	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4427001	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4521578	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4712122	0.84[TSI][hapmap]
rs4715600	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4715601	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4715605	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57818602	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6911260	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6940268	1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72870218	0.81[EUR][1000 genomes]
rs7746772	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7769092	1.00[YRI][hapmap]
rs9296836	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9382607	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9464373	0.89[ASN][1000 genomes]
rs9464374	0.89[ASN][1000 genomes]
rs9475653	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9475656	0.89[ASN][1000 genomes]
rs9475657	0.89[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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs724677	PAQR8	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56113400-56123800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr6:56117200-56123000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr6:56119800-56120800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr6:56120000-56120800	Enhancers	Fetal Brain Male	brain
5	chr6:56120200-56120800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr6:56120200-56120800	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr6:56120200-56120800	Enhancers	Aorta	Aorta
8	chr6:56120200-56120800	Enhancers	Fetal Muscle Leg	muscle
9	chr6:56120400-56120800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr6:56120400-56120800	Enhancers	HSMMtube	muscle
11	chr6:56120600-56123200	Weak transcription	Fetal Lung	lung
12	chr6:56120600-56123800	Weak transcription	Fetal Kidney	kidney

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