Variant report

Variant	rs9468189
Chromosome Location	chr6:27630611-27630612
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:27128425..27130087-chr6:27629956..27632184,2	MCF-7	breast:
2	chr6:27115470..27118070-chr6:27629887..27631658,2	K562	blood:
3	chr6:27617128..27618661-chr6:27630214..27631723,2	K562	blood:
4	chr6:27598921..27601744-chr6:27628779..27631198,2	K562	blood:
5	chr6:27623608..27625169-chr6:27628712..27630776,2	K562	blood:
6	chr6:27611027..27613554-chr6:27628187..27631088,2	K562	blood:
7	chr6:27625755..27627642-chr6:27629056..27632666,3	K562	blood:

Variant related genes	Relation type
ENSG00000238648	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1010261	0.82[YRI][hapmap]
rs12111051	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16867858	1.00[EUR][1000 genomes]
rs16867899	0.81[YRI][hapmap];1.00[EUR][1000 genomes]
rs16867901	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16867911	0.90[YRI][hapmap]
rs169263	1.00[EUR][1000 genomes]
rs2200870	1.00[EUR][1000 genomes]
rs4616979	0.82[AFR][1000 genomes]
rs55768730	1.00[EUR][1000 genomes]
rs55965630	1.00[EUR][1000 genomes]
rs55987929	1.00[EUR][1000 genomes]
rs56221999	1.00[EUR][1000 genomes]
rs56262840	1.00[EUR][1000 genomes]
rs56366090	1.00[EUR][1000 genomes]
rs58359716	1.00[EUR][1000 genomes]
rs58700542	1.00[EUR][1000 genomes]
rs60883433	0.91[AMR][1000 genomes]
rs6456800	1.00[EUR][1000 genomes]
rs6904979	1.00[EUR][1000 genomes]
rs73739117	1.00[EUR][1000 genomes]
rs73739122	1.00[EUR][1000 genomes]
rs73739150	1.00[EUR][1000 genomes]
rs73739606	1.00[EUR][1000 genomes]
rs73739685	1.00[EUR][1000 genomes]
rs73739750	1.00[EUR][1000 genomes]
rs73740805	1.00[EUR][1000 genomes]
rs73740842	1.00[EUR][1000 genomes]
rs73742455	1.00[EUR][1000 genomes]
rs9295739	1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9461396	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9468147	0.87[YRI][hapmap]
rs9468160	0.95[YRI][hapmap];0.82[AFR][1000 genomes]
rs9468190	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9468197	1.00[AMR][1000 genomes]
rs9468198	1.00[AMR][1000 genomes]
rs9468202	1.00[AMR][1000 genomes]
rs9468205	1.00[AMR][1000 genomes]
rs9468228	0.81[YRI][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	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	nsv883510	chr6:27550712-27730064	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
3	nsv1023673	chr6:27570731-27688782	Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	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
5	nsv1031337	chr6:27596676-27734884	Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
6	nsv525669	chr6:27623511-27657647	Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv883511	chr6:27623511-27660508	Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9468189	Hs.158943	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27627600-27631200	Weak transcription	Placenta	Placenta
2	chr6:27630200-27630800	Bivalent Enhancer	Brain Germinal Matrix	brain
3	chr6:27630400-27630800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr6:27630600-27630800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr6:27630600-27630800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr6:27630600-27631000	Enhancers	K562	blood

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