Variant report

Variant	rs10880811
Chromosome Location	chr12:45927546-45927547
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:45926815..45928655-chr12:46130897..46132547,2	MCF-7	breast:
2	chr12:45925922..45928759-chr12:45930090..45931726,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10785580	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10785581	0.87[EUR][1000 genomes]
rs10880810	0.88[CEU][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap]
rs10880814	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10880815	0.88[CEU][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs10880816	0.92[CEU][hapmap]
rs11183093	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11183094	0.88[CEU][hapmap]
rs11183097	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11183098	0.88[CEU][hapmap];0.80[MEX][hapmap];0.88[TSI][hapmap]
rs11183099	0.87[EUR][1000 genomes]
rs11183100	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11183101	0.83[EUR][1000 genomes]
rs11183102	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11183103	0.88[CEU][hapmap];0.87[YRI][hapmap];0.91[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs11183106	0.98[GIH][hapmap];0.88[MEX][hapmap]
rs1806689	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2897908	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs3958762	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs4277177	0.87[GIH][hapmap];0.88[MEX][hapmap]
rs4600280	0.87[EUR][1000 genomes]
rs4601849	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4606536	0.87[EUR][1000 genomes]
rs4768634	0.88[ASN][1000 genomes]
rs4768636	0.81[CEU][hapmap]
rs55987675	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56295584	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61923980	0.82[EUR][1000 genomes]
rs7296623	0.85[EUR][1000 genomes]
rs7303050	0.88[CEU][hapmap];0.88[EUR][1000 genomes]
rs7960483	0.88[CEU][hapmap];0.88[TSI][hapmap]
rs7971648	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832395	chr12:45841765-46039297	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv508672	chr12:45884730-45931091	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv691	chr12:45896295-45946455	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv1842210	chr12:45903118-45940761	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	esv3443760	chr12:45913734-45935783	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10880811	IRAK4	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:45924600-45927600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:45926200-45934400	Weak transcription	Thymus	Thymus
3	chr12:45926800-45933800	Weak transcription	Fetal Thymus	thymus

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