Variant report

Variant	rs12270261
Chromosome Location	chr11:120577413-120577414
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	chr11:120576655..120578167-chr11:120777548..120780496,2	MCF-7	breast:

Extended variants
information (count: 69 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10892616	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs11217987	0.81[CEU][hapmap]
rs11217988	0.81[CEU][hapmap]
rs11217989	0.81[CEU][hapmap]
rs12270409	0.81[CEU][hapmap]
rs12272864	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12273984	0.82[EUR][1000 genomes]
rs12274300	0.81[CEU][hapmap]
rs12276440	0.89[CEU][hapmap]
rs12278795	1.00[CEU][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes]
rs12280296	1.00[CEU][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12281001	1.00[ASN][1000 genomes]
rs12281008	1.00[ASN][1000 genomes]
rs12281464	0.90[CEU][hapmap]
rs12283240	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs12284730	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs12287882	1.00[ASN][1000 genomes]
rs12288261	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12291927	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12292552	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12293393	1.00[CEU][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12293509	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12294046	1.00[ASN][1000 genomes]
rs12294858	0.82[CEU][hapmap]
rs12295113	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12295200	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17124211	0.89[CEU][hapmap]
rs2846107	0.92[EUR][1000 genomes]
rs2846108	0.92[EUR][1000 genomes]
rs2846109	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs2852225	1.00[CEU][hapmap]
rs2852227	1.00[CEU][hapmap]
rs4567478	0.81[CEU][hapmap]
rs61901360	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61901361	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61901362	0.87[EUR][1000 genomes]
rs61901363	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61901364	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61901366	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61901367	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61901368	0.86[EUR][1000 genomes]
rs61901369	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61901370	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61901371	0.95[EUR][1000 genomes]
rs61901372	0.95[EUR][1000 genomes]
rs61901373	0.95[EUR][1000 genomes]
rs61901374	0.95[EUR][1000 genomes]
rs61901375	0.95[EUR][1000 genomes]
rs61901376	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61901377	0.94[EUR][1000 genomes]
rs61901378	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61901382	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61901398	0.92[EUR][1000 genomes]
rs61901399	0.92[EUR][1000 genomes]
rs61902683	1.00[ASN][1000 genomes]
rs61902686	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61902687	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61902689	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6589834	0.83[EUR][1000 genomes]
rs7102869	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7103228	0.81[CEU][hapmap]
rs7103418	0.90[CEU][hapmap]
rs7119619	0.81[CEU][hapmap]
rs7944756	0.90[CEU][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9630199	0.89[CEU][hapmap]
rs9630200	0.89[CEU][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	nsv1054407	chr11:120535570-120630114	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv1053607	chr11:120540795-120802006	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	esv3693392	chr11:120549745-120628012	Enhancers Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12270261	ARHGEF12	cis	cerebellum	SCAN
rs12270261	CBL	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:120568000-120580600	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr11:120570000-120581600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr11:120575200-120577800	Weak transcription	Ovary	ovary
4	chr11:120576200-120578000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr11:120577000-120578600	ZNF genes & repeats	Pancreas	Pancrea
6	chr11:120577200-120577800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr11:120577200-120578000	ZNF genes & repeats	Spleen	Spleen
8	chr11:120577400-120578800	Strong transcription	Fetal Lung	lung

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