Variant report

Variant	rs1375609
Chromosome Location	chr2:142871676-142871677
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:142870857..142873043-chr2:142887143..142889170,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168702	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs1001629	0.90[ASN][1000 genomes]
rs1011862	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10173643	0.91[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs10179841	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs10186258	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10190170	0.93[ASW][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.87[JPT][hapmap];0.98[LWK][hapmap];0.86[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap]
rs10203924	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10496913	0.85[CHB][hapmap]
rs10803487	0.85[CHB][hapmap]
rs10803489	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10928134	0.87[CHD][hapmap]
rs11680286	0.85[CHB][hapmap];0.92[CHD][hapmap];0.87[JPT][hapmap];0.83[MEX][hapmap]
rs11683745	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11688838	0.85[CHB][hapmap]
rs11691560	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs11691595	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[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]
rs12470890	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12472834	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12613064	0.85[JPT][hapmap]
rs12613097	0.85[JPT][hapmap]
rs12619411	0.89[CHB][hapmap]
rs13000270	0.82[ASN][1000 genomes]
rs13024219	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13036224	0.85[CHB][hapmap]
rs1349219	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1349220	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1349221	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1349222	0.89[ASN][1000 genomes]
rs1375606	0.95[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs1375611	0.89[CHB][hapmap];0.83[JPT][hapmap]
rs1375613	0.86[CHD][hapmap]
rs1375614	0.81[ASN][1000 genomes]
rs1449475	0.85[CHB][hapmap]
rs1449476	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1449477	0.85[CHB][hapmap];0.92[CHD][hapmap];0.87[JPT][hapmap]
rs1449478	0.85[CHB][hapmap];0.92[CHD][hapmap];0.87[JPT][hapmap]
rs1449480	0.93[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.86[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1449481	0.82[ASN][1000 genomes]
rs1449482	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs1449485	0.89[ASN][1000 genomes]
rs1449489	0.85[CHB][hapmap]
rs1449490	0.85[CHB][hapmap]
rs1449498	0.85[CHB][hapmap]
rs1449499	0.85[CHB][hapmap];0.87[CHD][hapmap]
rs1449501	0.85[CHB][hapmap];0.87[CHD][hapmap];0.82[MEX][hapmap]
rs1449503	0.90[CHB][hapmap];0.84[CHD][hapmap]
rs1449504	0.85[CHB][hapmap]
rs16848074	0.85[JPT][hapmap]
rs16848107	0.86[JPT][hapmap]
rs1868542	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1868543	0.85[CHB][hapmap]
rs1868544	0.85[CHB][hapmap]
rs1900933	0.85[CHB][hapmap];0.87[CHD][hapmap]
rs1900935	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1900936	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs2029142	0.85[CHB][hapmap];0.87[CHD][hapmap]
rs2060592	0.85[CHB][hapmap]
rs2167053	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2218734	0.85[CHB][hapmap]
rs2290140	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]
rs2381203	0.85[CHD][hapmap]
rs4662219	0.95[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs4662370	0.87[CHD][hapmap]
rs4662373	0.85[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs4662389	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62155598	0.89[ASN][1000 genomes]
rs6707136	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6712994	0.99[ASN][1000 genomes]
rs6744928	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs6754907	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs736602	0.90[CHB][hapmap]
rs7558803	0.81[CHB][hapmap];0.82[CHD][hapmap]
rs7565655	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7566250	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs7581031	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7586417	0.90[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs7598886	0.89[CHB][hapmap]
rs7605112	0.85[CHB][hapmap]
rs7608258	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7609479	0.93[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs9287332	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs957376	0.85[CHB][hapmap];0.92[CHD][hapmap];0.87[JPT][hapmap]
rs9941495	0.85[CHB][hapmap]
rs997123	0.84[ASN][1000 genomes]
rs9973706	1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[ASN][1000 genomes]

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
rs1375609	ZEB2	cis	cerebellum	SCAN

Chromatin state (count:4 , 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	chr2:142871000-142874600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr2:142871400-142873600	Weak transcription	Brain Substantia Nigra	brain

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