Variant report

Variant	rs1560016
Chromosome Location	chr12:87104070-87104071
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10431400	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10444513	0.94[ASN][1000 genomes]
rs10745430	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs10745432	0.94[JPT][hapmap]
rs10776992	0.83[JPT][hapmap]
rs10776999	0.83[ASN][1000 genomes]
rs10858463	1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[YRI][hapmap];0.95[ASN][1000 genomes]
rs10858465	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs10858468	0.89[CHB][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs1159292	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12299021	0.94[JPT][hapmap]
rs1469383	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs1560015	0.99[ASN][1000 genomes]
rs1863893	0.83[ASN][1000 genomes]
rs1981947	0.81[ASN][1000 genomes]
rs2013257	0.83[ASN][1000 genomes]
rs2016230	0.84[CHB][hapmap];0.83[JPT][hapmap]
rs2059773	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2081817	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs2114893	0.87[CHB][hapmap];0.87[JPT][hapmap]
rs2162670	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs2162673	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2162674	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs2195230	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2195231	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2406250	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs2406252	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs2406254	0.83[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs2406335	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2559814	0.88[CHB][hapmap];0.94[JPT][hapmap];0.83[YRI][hapmap];0.87[ASN][1000 genomes]
rs2702774	0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2702775	0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4240751	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs4465427	0.95[ASN][1000 genomes]
rs4583046	0.94[JPT][hapmap]
rs4842819	0.84[CHB][hapmap];0.83[JPT][hapmap]
rs4842820	0.82[JPT][hapmap]
rs717681	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7314362	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7314413	0.87[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7965979	0.90[ASN][1000 genomes]
rs7968485	0.83[ASN][1000 genomes]
rs7973223	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7977253	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs981142	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs982037	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2754127	chr12:86723232-87576932	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv899395	chr12:86813367-87177972	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv916862	chr12:86837694-87718558	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv899396	chr12:86863041-87276957	ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv899397	chr12:86863041-87636831	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv899399	chr12:86880442-87177972	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv916604	chr12:86966256-87275268	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv1049580	chr12:86966497-87354132	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv899400	chr12:87055983-87194443	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv1050699	chr12:87061020-87137487	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
11	nsv455681	chr12:87064588-87132840	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
12	nsv559691	chr12:87064588-87132840	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
13	nsv559692	chr12:87098055-87263693	Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:87101600-87106600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:87102600-87105600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr12:87104000-87104200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr12:87104000-87104200	Enhancers	HMEC	breast
5	chr12:87104000-87104400	ZNF genes & repeats	A549	lung

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