Variant report

Variant	rs9840098
Chromosome Location	chr3:54667349-54667350
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:54657347..54660339-chr3:54665865..54667406,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000229806	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs17081825	0.81[ASW][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28804505	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28829926	1.00[EUR][1000 genomes]
rs59697135	1.00[EUR][1000 genomes]
rs60521313	1.00[EUR][1000 genomes]
rs60564591	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9813045	1.00[EUR][1000 genomes]
rs9819282	0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9830638	1.00[MEX][hapmap]
rs9834511	1.00[EUR][1000 genomes]
rs9856685	1.00[MEX][hapmap]
rs9865838	1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs9989955	1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014595	chr3:53944473-54846754	Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv428084	chr3:54404258-54742756	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv834700	chr3:54637374-54803896	Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv525644	chr3:54653316-54709987	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54663000-54667800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:54663200-54667400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:54663600-54683800	Weak transcription	Stomach Smooth Muscle	stomach
4	chr3:54663800-54667400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:54663800-54667600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr3:54665200-54667800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr3:54665200-54672800	Weak transcription	Right Atrium	heart
8	chr3:54665400-54668200	Enhancers	Brain Germinal Matrix	brain
9	chr3:54665800-54667600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
10	chr3:54666200-54667800	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr3:54666400-54667600	Strong transcription	H9 Cell Line	embryonic stem cell
12	chr3:54666400-54667800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr3:54666400-54669000	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr3:54666800-54667800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
15	chr3:54667000-54668000	Genic enhancers	H1 Cell Line	embryonic stem cell
16	chr3:54667000-54668000	Genic enhancers	HUES6 Cell Line	embryonic stem cell
17	chr3:54667000-54668600	Transcr. at gene 5' and 3'	iPS-15b Cell Line	embryonic stem cell
18	chr3:54667200-54667800	Genic enhancers	HUES48 Cell Line	embryonic stem cell
19	chr3:54667200-54668200	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr3:54667200-54668200	Enhancers	HMEC	breast

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