Variant report

Variant	rs6892809
Chromosome Location	chr5:57111084-57111085
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	chr5:57105712..57108165-chr5:57110321..57113589,3	MCF-7	breast:

Extended variants
information (count: 60 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1016458	0.85[YRI][hapmap]
rs11738352	0.85[YRI][hapmap]
rs12519846	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12654378	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs1347072	0.90[CHB][hapmap];0.86[JPT][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1347073	0.90[CHB][hapmap];0.86[JPT][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1432477	0.90[CHB][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1432480	0.90[CHB][hapmap];0.86[JPT][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1432481	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1476938	0.85[YRI][hapmap]
rs16887464	0.96[CEU][hapmap];0.84[TSI][hapmap];0.90[EUR][1000 genomes]
rs16887469	0.90[EUR][1000 genomes]
rs1816391	0.99[ASN][1000 genomes]
rs1821211	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs1835873	0.85[ASN][1000 genomes]
rs1835875	0.86[ASN][1000 genomes]
rs1835876	0.99[ASN][1000 genomes]
rs2053013	0.86[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2215813	0.81[ASW][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.91[LWK][hapmap];0.84[MEX][hapmap];0.94[MKK][hapmap];0.89[TSI][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2408851	0.85[YRI][hapmap]
rs2408855	0.89[EUR][1000 genomes]
rs2539731	0.87[ASW][hapmap];0.82[LWK][hapmap];0.85[YRI][hapmap]
rs2539732	0.90[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.86[LWK][hapmap];0.84[MEX][hapmap];0.87[MKK][hapmap];0.89[TSI][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2539734	0.90[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs2568533	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2568534	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2568535	0.90[CHB][hapmap];0.85[JPT][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2568536	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2898030	0.99[ASN][1000 genomes]
rs2898031	0.97[ASN][1000 genomes]
rs2898032	0.89[ASN][1000 genomes]
rs34152283	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34397458	0.90[EUR][1000 genomes]
rs34711481	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35483666	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4700229	0.99[ASN][1000 genomes]
rs4700230	0.99[ASN][1000 genomes]
rs62360111	0.94[ASN][1000 genomes]
rs6450440	0.93[ASN][1000 genomes]
rs6450441	0.94[ASN][1000 genomes]
rs6868222	0.96[CEU][hapmap];0.84[TSI][hapmap];0.89[EUR][1000 genomes]
rs6887425	0.83[YRI][hapmap]
rs757635	0.81[ASW][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.91[LWK][hapmap];0.94[MKK][hapmap];0.89[TSI][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7701201	0.87[ASN][1000 genomes]
rs7717208	0.87[EUR][1000 genomes]
rs7721249	0.96[CEU][hapmap];0.84[TSI][hapmap];0.87[EUR][1000 genomes]
rs7722730	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs854025	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs854026	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs854027	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs854030	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs854032	0.85[ASN][1000 genomes]
rs854034	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs887868	0.90[CHB][hapmap];0.86[JPT][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs987671	0.85[YRI][hapmap]
rs988658	0.90[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.89[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525330	chr5:56931673-57320343	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	esv2756302	chr5:56978143-57180143	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv830310	chr5:56989346-57176006	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv2763454	chr5:57006531-57161140	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6892809	PLK2	cis	cerebellum	SCAN
rs6892809	GPX8	cis	parietal	SCAN
rs6892809	DHX29	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:57100600-57111600	Weak transcription	HSMM	muscle
2	chr5:57101600-57111600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr5:57102400-57112000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr5:57105600-57112200	Weak transcription	NHLF	lung
5	chr5:57108200-57111600	Weak transcription	NHDF-Ad	bronchial
6	chr5:57108400-57111600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr5:57108400-57111600	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr5:57108800-57111600	Weak transcription	Osteobl	bone
9	chr5:57109800-57112000	Weak transcription	Fetal Heart	heart
10	chr5:57110800-57113200	Enhancers	iPS-15b Cell Line	embryonic stem cell

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