Variant report

Variant	rs10056565
Chromosome Location	chr5:80619046-80619047
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	chr5:80617420..80619692-chr5:80645550..80648480,2	K562	blood:

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10038684	0.83[ASN][1000 genomes]
rs10041063	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs10041138	0.81[CEU][hapmap]
rs10052929	0.85[CEU][hapmap]
rs10053706	0.83[ASN][1000 genomes]
rs10061143	0.82[CEU][hapmap]
rs10063615	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10066296	0.83[ASN][1000 genomes]
rs10078279	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs10474656	0.83[ASN][1000 genomes]
rs10514213	1.00[CHB][hapmap]
rs1055383	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs10942945	1.00[CHB][hapmap]
rs11950033	1.00[CHB][hapmap]
rs13362314	0.83[ASN][1000 genomes]
rs1566432	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs1566433	0.85[CEU][hapmap]
rs17294418	1.00[CHB][hapmap]
rs2173697	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2270823	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs2406556	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28464111	0.83[ASN][1000 genomes]
rs28650401	0.83[ASN][1000 genomes]
rs2897389	1.00[CHB][hapmap]
rs2897390	1.00[CHB][hapmap]
rs3756636	0.84[CEU][hapmap]
rs4703827	1.00[CHB][hapmap]
rs4704707	1.00[CHB][hapmap]
rs4704710	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs4704711	0.87[CEU][hapmap]
rs4704712	0.83[ASN][1000 genomes]
rs4704714	0.85[CEU][hapmap]
rs4704715	0.83[ASN][1000 genomes]
rs4704720	0.92[ASN][1000 genomes]
rs59132806	0.83[ASN][1000 genomes]
rs60488995	0.83[ASN][1000 genomes]
rs60904680	0.83[ASN][1000 genomes]
rs61244991	0.83[ASN][1000 genomes]
rs62365865	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68077638	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6863732	0.85[CEU][hapmap]
rs6866499	1.00[CHB][hapmap]
rs6867884	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6885028	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6893467	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs7709071	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7709149	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7720009	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs7734902	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs921928	1.00[CHB][hapmap]
rs9293841	1.00[CHB][hapmap];0.83[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	nsv1024844	chr5:79862428-80860430	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10056565	ZCCHC9	cis	multi-tissue	Pritchard
rs10056565	HSS00347093	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80608600-80623000	Weak transcription	Psoas Muscle	Psoas
2	chr5:80610600-80621800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr5:80611600-80623600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr5:80612200-80623600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr5:80618800-80619600	Strong transcription	Liver	Liver
6	chr5:80619000-80619400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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