Variant report

Variant	rs2056638
Chromosome Location	chr12:85422437-85422438
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	chr12:85268551..85271336-chr12:85421363..85424699,4	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1031190	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11116694	0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.83[YRI][hapmap]
rs12227853	1.00[CEU][hapmap];0.95[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap]
rs12301980	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12304556	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1404871	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1494500	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1494501	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1507209	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1525548	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs168613	0.95[CEU][hapmap];0.88[CHB][hapmap];0.83[JPT][hapmap]
rs168615	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1690835	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1852148	1.00[CEU][hapmap];0.81[GIH][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1973816	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2660449	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2660454	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2660455	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2660459	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2708496	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2708498	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs359992	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap]
rs6539879	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6539881	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7132596	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7133817	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7302312	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7316900	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs777035	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs7954110	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7962411	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7962577	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs796567	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap]
rs7974418	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]

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	nsv899377	chr12:85157346-85629241	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1040452	chr12:85179586-85747907	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	esv1792335	chr12:85321249-86003609	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2056638	MYF5	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:85422400-85422800	Enhancers	Thymus	Thymus
2	chr12:85422400-85423000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr12:85422400-85423000	Enhancers	Brain Hippocampus Middle	brain
4	chr12:85422400-85423400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr12:85422400-85423400	Enhancers	Hela-S3	cervix

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