Variant report

Variant	rs27840
Chromosome Location	chr5:57655814-57655815
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	chr5:57654875..57656894-chr5:57657997..57659625,2	MCF-7	breast:

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10513142	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11739229	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11740115	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11742895	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11745076	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11748388	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13157907	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13159047	0.89[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1469090	0.81[AFR][1000 genomes]
rs151868	0.81[AFR][1000 genomes]
rs151888	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs152010	1.00[YRI][hapmap]
rs154476	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs154670	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs154671	0.81[AFR][1000 genomes]
rs154673	0.81[AFR][1000 genomes]
rs17709103	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17765852	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs181745	0.92[GIH][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs181954	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1974849	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2081087	0.81[AFR][1000 genomes]
rs2434584	0.81[AFR][1000 genomes]
rs245282	0.81[AFR][1000 genomes]
rs245285	1.00[YRI][hapmap]
rs245287	0.81[AFR][1000 genomes]
rs245295	0.81[AFR][1000 genomes]
rs245493	0.81[LWK][hapmap];1.00[YRI][hapmap]
rs27210	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs27211	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2910577	0.81[AFR][1000 genomes]
rs2910592	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs2910600	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs2910605	1.00[YRI][hapmap]
rs2964193	0.81[AFR][1000 genomes]
rs2964200	0.81[AFR][1000 genomes]
rs34434884	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35263833	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35398083	0.80[EUR][1000 genomes]
rs35491600	0.94[EUR][1000 genomes]
rs35521508	0.81[EUR][1000 genomes]
rs35988720	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs36120901	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36179294	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs37484	0.81[AFR][1000 genomes]
rs37485	0.81[AFR][1000 genomes]
rs37486	0.81[AFR][1000 genomes]
rs37488	0.81[AFR][1000 genomes]
rs37492	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs37516	0.81[AFR][1000 genomes]
rs37523	0.81[AFR][1000 genomes]
rs37526	0.81[AFR][1000 genomes]
rs37527	0.81[AFR][1000 genomes]
rs37528	0.81[AFR][1000 genomes]
rs37533	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs37536	0.81[AFR][1000 genomes]
rs3846535	0.94[EUR][1000 genomes]
rs40209	0.81[AFR][1000 genomes]
rs40210	0.81[AFR][1000 genomes]
rs4099272	0.94[EUR][1000 genomes]
rs4099273	0.94[EUR][1000 genomes]
rs41384	0.82[GIH][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs58174847	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67884475	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71624201	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs905199	0.94[EUR][1000 genomes]
rs931745	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs986459	0.94[EUR][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	esv3489100	chr5:57545689-57669673	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	esv3489101	chr5:57545689-57669673	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv4842	chr5:57653257-57694850	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs27840	GZMK	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:57650400-57656000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr5:57651800-57656400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr5:57655600-57656400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr5:57655800-57656800	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr5:57655800-57657200	Enhancers	H1 Cell Line	embryonic stem cell

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