Variant report

Variant	rs12240590
Chromosome Location	chr10:99072066-99072067
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr10:99072051-99072106	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:99070639..99072420-chr10:99078021..99080408,2	MCF-7	breast:
2	chr10:99069668..99072343-chr10:99094033..99096294,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000237169	TF binding region
ENSG00000181274	Chromatin interaction
ENSG00000165879	Chromatin interaction
ENSG00000225850	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1088187	0.81[EUR][1000 genomes]
rs11189121	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1253386	0.81[EUR][1000 genomes]
rs1253387	0.88[EUR][1000 genomes]
rs1253396	0.85[EUR][1000 genomes]
rs1253397	0.85[EUR][1000 genomes]
rs1253400	0.84[EUR][1000 genomes]
rs1253401	0.84[CEU][hapmap];0.85[EUR][1000 genomes]
rs12769073	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12782676	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13439	1.00[CEU][hapmap];0.86[GIH][hapmap];0.89[TSI][hapmap]
rs1890966	0.81[EUR][1000 genomes]
rs2484880	1.00[CEU][hapmap]
rs2861877	0.86[EUR][1000 genomes]
rs2992773	0.83[EUR][1000 genomes]
rs34115590	0.86[EUR][1000 genomes]
rs34288920	0.86[EUR][1000 genomes]
rs34624597	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs36098270	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4917765	0.83[EUR][1000 genomes]
rs61569149	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61861842	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61861843	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61861844	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61861849	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61861850	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs701821	0.90[CEU][hapmap];0.86[TSI][hapmap]
rs7074896	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7091162	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7101333	0.86[EUR][1000 genomes]
rs7915926	0.90[CEU][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs793515	0.84[CEU][hapmap];0.86[TSI][hapmap]
rs793516	0.95[CEU][hapmap]
rs793517	0.95[CEU][hapmap];0.84[GIH][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap]
rs793519	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs793520	1.00[CEU][hapmap];0.86[GIH][hapmap];0.86[TSI][hapmap];0.88[EUR][1000 genomes]
rs793522	0.81[EUR][1000 genomes]
rs793524	1.00[CEU][hapmap];0.86[GIH][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs793531	0.83[EUR][1000 genomes]
rs796980	0.88[EUR][1000 genomes]
rs946981	1.00[CEU][hapmap];0.86[GIH][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532232	chr10:98360775-99141797	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv1041614	chr10:98928281-99083056	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv1045553	chr10:98944397-99122203	Strong transcription Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv540750	chr10:98944397-99122203	Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv831952	chr10:98998344-99145924	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv895914	chr10:99006083-99131676	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv948156	chr10:99067716-99072148	Weak transcription Bivalent Enhancer Enhancers	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	nsv825533	chr10:99070570-99115599	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12240590	FRAT1	cis	multi-tissue	Pritchard
rs12240590	KIAA0690	cis	multi-tissue	Pritchard
rs12240590	EXOSC1	cis	parietal	SCAN
rs12240590	FRAT2	cis	multi-tissue	Pritchard
rs12240590	RRP12	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:99068800-99072800	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr10:99069000-99073200	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr10:99069000-99073600	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr10:99069800-99075400	Weak transcription	HepG2	liver
5	chr10:99072000-99073000	Enhancers	K562	blood

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