Variant report

Variant	rs2290140
Chromosome Location	chr2:142876051-142876052
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	chr2:142874759..142876508-chr2:142879340..142881781,2	MCF-7	breast:

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1011862	0.80[EUR][1000 genomes]
rs10175827	0.91[JPT][hapmap]
rs10179841	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs10186258	0.83[EUR][1000 genomes]
rs10190170	0.90[CHD][hapmap];0.86[MEX][hapmap]
rs10203924	0.83[EUR][1000 genomes]
rs10496912	0.92[JPT][hapmap]
rs10496913	0.94[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs10803489	0.83[EUR][1000 genomes]
rs11680286	0.85[CHD][hapmap];0.87[MEX][hapmap];0.83[YRI][hapmap]
rs11683745	0.83[EUR][1000 genomes]
rs11691560	0.83[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap]
rs11691595	0.83[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap]
rs12470890	0.83[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap]
rs12472834	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12613064	0.84[JPT][hapmap]
rs12613097	0.83[JPT][hapmap]
rs12619411	0.88[CHB][hapmap]
rs12988578	0.88[ASN][1000 genomes]
rs13024219	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13429550	0.90[JPT][hapmap]
rs1349219	0.86[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes]
rs1349220	0.82[EUR][1000 genomes]
rs1349221	0.83[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes]
rs1375606	0.84[CHB][hapmap]
rs1375609	0.82[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs1375611	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1375612	0.85[JPT][hapmap];0.82[YRI][hapmap];0.85[ASN][1000 genomes]
rs1375613	0.93[CHD][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs1375614	0.82[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1449476	0.82[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap]
rs1449477	0.84[CHD][hapmap]
rs1449478	0.85[CHD][hapmap];0.82[MEX][hapmap]
rs1449480	0.84[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap]
rs1449482	0.83[YRI][hapmap]
rs1449499	0.83[MEX][hapmap]
rs1449501	0.87[MEX][hapmap]
rs1449503	0.80[CHB][hapmap]
rs16848074	0.83[JPT][hapmap]
rs16848107	0.84[JPT][hapmap]
rs17826042	0.92[JPT][hapmap]
rs1868542	0.83[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap]
rs1900935	0.83[EUR][1000 genomes]
rs1900936	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2029142	0.83[MEX][hapmap]
rs2167053	0.90[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs2381203	0.81[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.85[ASN][1000 genomes]
rs4662219	0.95[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];0.82[MEX][hapmap]
rs4662389	0.83[EUR][1000 genomes]
rs4662396	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs62155638	0.85[ASN][1000 genomes]
rs6707136	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6744928	0.90[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.82[MEX][hapmap]
rs736602	0.89[CHB][hapmap]
rs7565655	0.83[EUR][1000 genomes]
rs7566250	0.80[YRI][hapmap]
rs7581031	0.87[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap]
rs7586417	0.89[CHB][hapmap];0.92[JPT][hapmap]
rs7608258	0.87[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap]
rs7609479	0.84[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap]
rs9287332	0.83[EUR][1000 genomes]
rs957376	0.85[CHD][hapmap];0.82[MEX][hapmap]
rs970600	0.92[JPT][hapmap];0.83[MEX][hapmap]
rs970601	0.92[JPT][hapmap]
rs9973706	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997274	chr2:142760393-143599193	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv526107	chr2:142768518-142884248	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv875254	chr2:142833327-142931146	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1006247	chr2:142851056-143289465	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2290140	ZEB2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:142870000-142878400	Weak transcription	Brain Hippocampus Middle	brain
2	chr2:142870800-142877400	Weak transcription	Brain Anterior Caudate	brain
3	chr2:142875200-142876400	Enhancers	Brain Substantia Nigra	brain

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