Variant report

Variant	rs10878553
Chromosome Location	chr12:67446079-67446080
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10459266	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10784605	0.83[ASN][1000 genomes]
rs10784606	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10784607	0.83[ASN][1000 genomes]
rs10784608	0.83[ASN][1000 genomes]
rs10784609	0.83[ASN][1000 genomes]
rs10878559	0.83[ASN][1000 genomes]
rs10878560	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10878561	0.83[ASN][1000 genomes]
rs10878566	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1104655	0.81[CEU][hapmap]
rs11176552	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11176555	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11176556	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11176557	0.96[ASN][1000 genomes]
rs11176562	0.89[ASN][1000 genomes]
rs11176567	0.86[ASN][1000 genomes]
rs11176580	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11176582	0.81[ASN][1000 genomes]
rs11176586	0.83[ASN][1000 genomes]
rs11611265	0.89[CEU][hapmap]
rs11829047	0.83[ASN][1000 genomes]
rs12227624	0.83[ASN][1000 genomes]
rs12227692	0.86[ASN][1000 genomes]
rs12228046	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12228922	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12228998	0.84[ASN][1000 genomes]
rs12230670	0.83[ASN][1000 genomes]
rs12231102	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12833688	0.83[ASN][1000 genomes]
rs1465026	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1526835	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1526839	0.83[ASN][1000 genomes]
rs1589971	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17103378	0.85[CEU][hapmap]
rs17183558	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs17183565	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs17183669	0.92[CEU][hapmap]
rs17183676	0.84[CEU][hapmap]
rs17183711	0.85[CEU][hapmap]
rs17781064	0.80[EUR][1000 genomes]
rs17781196	0.92[CEU][hapmap]
rs2870926	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4244070	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4913529	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6581735	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6581740	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7136952	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7138249	1.00[ASN][1000 genomes]
rs7298268	0.89[ASN][1000 genomes]
rs7311137	0.84[ASN][1000 genomes]
rs7953961	0.95[ASN][1000 genomes]
rs7959866	1.00[ASN][1000 genomes]
rs7961562	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7961790	0.84[ASN][1000 genomes]
rs7961954	0.84[ASN][1000 genomes]
rs7962241	0.84[ASN][1000 genomes]
rs7974866	0.83[ASN][1000 genomes]
rs7980101	0.84[ASN][1000 genomes]
rs941096	0.84[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	nsv541524	chr12:67311057-67700349	Strong transcription Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv469462	chr12:67361657-67475906	Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv559211	chr12:67361657-67475906	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv559212	chr12:67373549-67850925	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:67437000-67446600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:67437000-67446800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr12:67437000-67446800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr12:67437000-67446800	Weak transcription	HMEC	breast
5	chr12:67437000-67450200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr12:67440200-67447200	Weak transcription	Placenta	Placenta
7	chr12:67440200-67448600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr12:67440200-67461200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr12:67446000-67446400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr12:67446000-67449000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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