Variant report

Variant	rs9468228
Chromosome Location	chr6:27748949-27748950
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs187995	1.00[EUR][1000 genomes]
rs200470	0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs200472	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs200947	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs200955	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs200959	1.00[EUR][1000 genomes]
rs200982	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs200984	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs201003	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs201005	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56342784	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59716769	1.00[EUR][1000 genomes]
rs7740062	1.00[EUR][1000 genomes]
rs9468189	0.81[YRI][hapmap]
rs9468190	0.81[YRI][hapmap]
rs9468198	1.00[EUR][1000 genomes]
rs9468205	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv981120	chr6:27746371-27751747	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	8 gene(s)	inside rSNPs	n/a
8	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
rs9468228	Hs.158943	cis	multi-tissue	Pritchard

Chromatin state (count:5 , 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	chr6:27745600-27753200	Weak transcription	HepG2	liver
3	chr6:27747000-27750000	Weak transcription	K562	blood
4	chr6:27748800-27749000	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
5	chr6:27748800-27754600	Enhancers	Rectal Mucosa Donor 31	rectum

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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