Variant report

Variant	rs666846
Chromosome Location	chr6:27755903-27755904
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:27750078..27752757-chr6:27753756..27756420,3	MCF-7	breast:
2	chr6:27754884..27756658-chr6:28667603..28670303,2	K562	blood:
3	chr6:27745777..27747723-chr6:27753889..27756682,2	MCF-7	breast:
4	chr6:27109661..27117801-chr6:27755492..27760111,8	K562	blood:
5	chr6:27754992..27756885-chr6:27838011..27840900,2	MCF-7	breast:
6	chr6:27753667..27756583-chr6:27759368..27762944,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000184825	Chromatin interaction
ENSG00000182572	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000265565	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1015075	0.85[JPT][hapmap]
rs12174918	0.91[ASN][1000 genomes]
rs175597	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs183225	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs200466	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs200469	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs200471	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs200473	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs200478	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs200479	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]
rs200481	0.89[ASN][1000 genomes]
rs200482	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs200483	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs200484	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	1.00[JPT][hapmap]
rs200497	0.83[ASN][1000 genomes]
rs200498	0.81[ASN][1000 genomes]
rs200501	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs200948	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	1.00[JPT][hapmap]
rs200954	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs200965	1.00[JPT][hapmap]
rs200968	1.00[JPT][hapmap]
rs200973	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	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs200990	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs200992	0.83[ASN][1000 genomes]
rs200995	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs200996	0.85[ASN][1000 genomes]
rs201002	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2277104	0.83[ASN][1000 genomes]
rs2394001	0.91[ASN][1000 genomes]
rs2747054	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs34295134	0.85[ASN][1000 genomes]
rs36108923	0.85[ASN][1000 genomes]
rs370155	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs390764	0.87[ASN][1000 genomes]
rs401754	0.87[ASN][1000 genomes]
rs401763	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	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56002038	0.87[EUR][1000 genomes]
rs56870390	0.85[ASN][1000 genomes]
rs59015666	0.91[ASN][1000 genomes]
rs59199903	0.87[EUR][1000 genomes]
rs6901437	0.87[EUR][1000 genomes]
rs6901712	0.87[EUR][1000 genomes]
rs6906980	0.81[EUR][1000 genomes]
rs6915101	0.87[EUR][1000 genomes]
rs6936952	0.87[EUR][1000 genomes]
rs6938018	0.87[EUR][1000 genomes]
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	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]
rs9468227	0.85[YRI][hapmap];0.87[EUR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs666846	Hs.158943	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27751600-27759200	Weak transcription	Colonic Mucosa	Colon
2	chr6:27753800-27759000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr6:27754000-27759200	Weak transcription	HepG2	liver
4	chr6:27754200-27759000	Weak transcription	Fetal Intestine Large	intestine
5	chr6:27754600-27759000	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr6:27755200-27759200	Weak transcription	K562	blood

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