Variant report

Variant	rs6580099
Chromosome Location	chr5:154055507-154055508
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:154054874..154057570-chr5:154132622..154134440,2	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10039709	0.80[CEU][hapmap]
rs10875591	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11167698	0.83[ASN][1000 genomes]
rs12515092	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12652072	0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs1862130	0.83[ASN][1000 genomes]
rs1972616	0.83[ASN][1000 genomes]
rs2396995	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28794278	0.86[ASN][1000 genomes]
rs4958382	0.80[CEU][hapmap];0.89[CHB][hapmap];0.83[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4958758	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4958759	0.84[CHB][hapmap];0.83[JPT][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4958761	0.80[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];0.84[GIH][hapmap];0.83[JPT][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6580111	0.80[CEU][hapmap]
rs6868098	0.80[CEU][hapmap]
rs7444282	0.88[ASN][1000 genomes]
rs7445576	0.83[ASN][1000 genomes]
rs749777	0.80[CEU][hapmap];0.86[CHD][hapmap]
rs918365	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9324791	0.87[CHB][hapmap]
rs9324792	0.80[CEU][hapmap];0.83[CHD][hapmap];0.80[GIH][hapmap]
rs965235	0.80[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];0.83[JPT][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][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	esv3401644	chr5:153898681-154058368	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
2	nsv462491	chr5:154045280-154066205	Flanking Active TSS Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
3	nsv600090	chr5:154045280-154066205	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6580099	SYNPO	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:154042800-154061600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:154048600-154062000	Weak transcription	Right Atrium	heart
3	chr5:154053600-154057400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr5:154054000-154062000	Weak transcription	Primary hematopoietic stem cells	blood
5	chr5:154055000-154057800	Enhancers	Pancreas	Pancrea
6	chr5:154055000-154059000	Weak transcription	H9 Cell Line	embryonic stem cell

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