Variant report

Variant	rs9468227
Chromosome Location	chr6:27746342-27746343
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr6:27640023..27641609-chr6:27744727..27746412,2	K562	blood:
2	chr6:27461978..27463563-chr6:27744301..27746788,2	K562	blood:
3	chr6:27744761..27747867-chr6:27758538..27761675,3	MCF-7	breast:
4	chr6:27744586..27748272-chr6:27756903..27759108,3	MCF-7	breast:
5	chr6:27739073..27741027-chr6:27745777..27747654,2	MCF-7	breast:
6	chr6:27106342..27108583-chr6:27745560..27747825,2	K562	blood:
7	chr6:27481158..27483967-chr6:27745057..27747671,2	K562	blood:
8	chr6:27461978..27464683-chr6:27744618..27746788,2	K562	blood:
9	chr6:27100313..27102591-chr6:27743747..27746593,3	K562	blood:
10	chr6:27745777..27747723-chr6:27753889..27756682,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000270666	Chromatin interaction
ENSG00000198339	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000124635	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11962485	1.00[CEU][hapmap]
rs11962868	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs11966528	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs11966565	1.00[ASN][1000 genomes]
rs11968469	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11970638	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs183225	0.85[YRI][hapmap]
rs200466	0.86[YRI][hapmap];0.87[EUR][1000 genomes]
rs200469	0.87[EUR][1000 genomes]
rs200471	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes]
rs200473	0.87[EUR][1000 genomes]
rs480699	0.81[AFR][1000 genomes]
rs56002038	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59199903	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60339576	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs666846	0.85[YRI][hapmap];0.87[EUR][1000 genomes]
rs6901437	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6901712	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6906904	1.00[ASN][1000 genomes]
rs6906980	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6908615	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6915101	1.00[CEU][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6922530	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs6933702	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs6936952	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6938018	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73384331	1.00[ASN][1000 genomes]
rs73389017	1.00[ASN][1000 genomes]
rs73389037	1.00[ASN][1000 genomes]
rs73389068	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7742752	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461422	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs9468262	1.00[CEU][hapmap];1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9468227	Hs.158943	cis	multi-tissue	Pritchard

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27743600-27750000	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr6:27744200-27746400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr6:27745600-27746600	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr6:27745600-27746600	Weak transcription	A549	lung
5	chr6:27745600-27746600	Active TSS	K562	blood
6	chr6:27745600-27746800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:27745600-27753200	Weak transcription	HepG2	liver
8	chr6:27746200-27748400	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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