Variant report

Variant	rs12080991
Chromosome Location	chr1:179242140-179242141
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	chr1:179241287..179243492-chr1:179260059..179262994,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000057252	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1004959	0.92[ASN][1000 genomes]
rs10157885	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1173077	0.83[YRI][hapmap]
rs12143004	1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap]
rs13306729	0.81[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap]
rs16854064	1.00[GIH][hapmap];0.82[MEX][hapmap]
rs17277358	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[ASN][1000 genomes]
rs17361990	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs17362128	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2017688	0.83[ASN][1000 genomes]
rs2274230	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[ASN][1000 genomes]
rs28459842	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28914474	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28914485	0.86[ASN][1000 genomes]
rs3753532	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs55642919	0.86[ASN][1000 genomes]
rs55825882	0.83[ASN][1000 genomes]
rs55827544	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55920203	0.83[ASN][1000 genomes]
rs55955319	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56382583	0.86[ASN][1000 genomes]
rs60741626	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60826716	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6668200	1.00[CEU][hapmap]
rs6669988	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9650997	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[ASN][1000 genomes]
rs9724754	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];0.83[ASN][1000 genomes]
rs9725888	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs9803885	0.84[EUR][1000 genomes];0.97[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	nsv1005278	chr1:179197645-179371395	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12080991	IRF1	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179241200-179242400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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