Variant report

Variant	rs200479
Chromosome Location	chr6:27771684-27771685
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:27112242..27117659-chr6:27770082..27780470,17	MCF-7	breast:
2	chr6:27099709..27101430-chr6:27771176..27773201,2	MCF-7	breast:
3	chr6:27093369..27111594-chr6:27770152..27782376,64	K562	blood:
4	chr6:27093465..27120217-chr6:27768366..27817187,256	K562	blood:
5	chr6:27140467..27142288-chr6:27771124..27773202,2	K562	blood:
6	chr6:27111360..27127716-chr6:27768319..27787545,69	MCF-7	breast:
7	chr6:27112544..27118917-chr6:27770503..27773854,7	K562	blood:

Variant related genes	Relation type
ENSG00000196787	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000198339	Chromatin interaction
ENSG00000265565	Chromatin interaction
ENSG00000124635	Chromatin interaction
ENSG00000197903	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1015075	0.85[JPT][hapmap]
rs12174918	0.91[ASN][1000 genomes]
rs175597	0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs183225	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs200466	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs200469	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs200471	0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs200473	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs200478	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs200481	0.94[CHD][hapmap];0.89[ASN][1000 genomes]
rs200482	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs200483	0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs200484	0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs200485	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs200488	0.85[ASN][1000 genomes]
rs200489	0.85[ASN][1000 genomes]
rs200490	0.88[CHD][hapmap];1.00[JPT][hapmap]
rs200497	0.83[ASN][1000 genomes]
rs200498	0.81[ASN][1000 genomes]
rs200501	0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs200948	0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs200949	1.00[JPT][hapmap]
rs200950	0.81[ASN][1000 genomes]
rs200952	0.81[ASN][1000 genomes]
rs200953	0.94[CHD][hapmap];1.00[JPT][hapmap]
rs200954	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs200965	1.00[JPT][hapmap]
rs200968	0.94[CHD][hapmap];1.00[JPT][hapmap]
rs200973	0.94[CHD][hapmap];1.00[JPT][hapmap]
rs200974	1.00[JPT][hapmap]
rs200975	1.00[JPT][hapmap]
rs200977	1.00[JPT][hapmap]
rs200981	1.00[JPT][hapmap]
rs200983	0.85[ASN][1000 genomes]
rs200989	0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs200990	0.94[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs200992	0.83[ASN][1000 genomes]
rs200995	0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs200996	0.85[ASN][1000 genomes]
rs201002	0.94[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2277104	0.83[ASN][1000 genomes]
rs2394001	0.91[ASN][1000 genomes]
rs2747054	0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs34295134	0.85[ASN][1000 genomes]
rs36108923	0.85[ASN][1000 genomes]
rs370155	0.94[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs390764	0.87[ASN][1000 genomes]
rs401754	0.87[ASN][1000 genomes]
rs401763	0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4713122	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4713124	0.91[ASN][1000 genomes]
rs480699	0.92[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs56870390	0.85[ASN][1000 genomes]
rs59015666	0.91[ASN][1000 genomes]
rs666846	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6901437	0.96[MKK][hapmap];0.87[TSI][hapmap]
rs6915101	0.98[MKK][hapmap];0.87[TSI][hapmap]
rs904142	0.85[JPT][hapmap]
rs9348779	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9357052	1.00[JPT][hapmap]
rs9368531	0.87[ASN][1000 genomes]
rs9368534	0.83[ASN][1000 genomes]
rs9368535	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9368536	0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9368537	0.85[JPT][hapmap]
rs9380018	0.89[ASN][1000 genomes]
rs9380026	1.00[JPT][hapmap]
rs9380028	0.85[JPT][hapmap]
rs9380030	0.85[JPT][hapmap]
rs9393858	0.87[ASN][1000 genomes]

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	nsv1022797	chr6:27396961-27864277	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	390 gene(s)	inside rSNPs	diseases
2	nsv830618	chr6:27593274-27789605	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	143 gene(s)	inside rSNPs	diseases
3	nsv432858	chr6:27719375-28011652	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	387 gene(s)	inside rSNPs	diseases
4	nsv1017440	chr6:27734824-27864277	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	370 gene(s)	inside rSNPs	diseases
5	nsv1022173	chr6:27734824-27959408	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	379 gene(s)	inside rSNPs	diseases
6	nsv1017057	chr6:27745777-27789683	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	125 gene(s)	inside rSNPs	diseases
7	nsv883512	chr6:27748631-27969004	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	379 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs200479	Hs.158943	cis	multi-tissue	Pritchard
rs200479	HIST1H4J	cis	lymphoblastoid	seeQTL

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27764400-27774200	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr6:27769200-27774400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr6:27769200-27774400	Weak transcription	NHEK	skin
4	chr6:27769400-27772600	Weak transcription	K562	blood
5	chr6:27769600-27774400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr6:27771400-27771800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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