Variant report

Variant	rs154564
Chromosome Location	chr5:89883820-89883821
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:89881845..89884640-chr5:89908883..89910553,2	K562	blood:
2	chr5:89878566..89881386-chr5:89882333..89884727,3	K562	blood:
3	chr5:89881685..89883243-chr5:89883707..89886332,2	K562	blood:
4	chr5:89702901..89704875-chr5:89883811..89886789,2	K562	blood:
5	chr5:89852793..89854346-chr5:89883740..89885331,2	MCF-7	breast:
6	chr5:89878566..89881617-chr5:89882501..89884794,5	K562	blood:
7	chr5:89883022..89885296-chr5:89901095..89903175,2	K562	blood:

Variant related genes	Relation type
ENSG00000153140	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10044044	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10462487	0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10462488	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10462489	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11952742	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11955749	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1344030	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs152714	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs152715	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs154556	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs154557	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs154558	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs154559	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs154561	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs154562	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs154563	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs154565	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs154571	0.93[GIH][hapmap];0.89[JPT][hapmap]
rs16868839	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16868892	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16868894	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16868901	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16868903	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs168743	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs171629	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs173660	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.90[TSI][hapmap];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs187278	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs189691	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2366776	0.87[CEU][hapmap];0.87[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs250367	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs250371	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs257848	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs40205	0.84[JPT][hapmap]
rs45478296	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs45507696	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4916680	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4916803	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4916804	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4916805	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4916807	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55918113	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56002033	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56360530	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57437217	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58132310	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58598764	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59496152	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60359999	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60651883	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66977476	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67556741	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs68045375	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs68096329	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6889828	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72782722	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7701844	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7707357	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7709691	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9293546	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.90[TSI][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs950692	0.82[CHD][hapmap];0.90[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021142	chr5:89102893-89897826	Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv537804	chr5:89102893-89897826	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv432750	chr5:89410113-90137144	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv432751	chr5:89457044-90090444	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	nsv529544	chr5:89523963-90412409	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
6	nsv882366	chr5:89826726-89894564	Bivalent/Poised TSS Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
7	nsv933668	chr5:89854253-89999672	Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 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	chr5:89859400-89884200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr5:89867400-89889200	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr5:89868800-89884400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr5:89882000-89887600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr5:89882600-89884200	Weak transcription	K562	blood
6	chr5:89882600-89884400	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr5:89882600-89886000	Weak transcription	Placenta	Placenta
8	chr5:89882600-89887400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr5:89882800-89888800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr5:89883000-89887400	Weak transcription	HUES48 Cell Line	embryonic stem cell

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