Variant report

Variant	rs557789
Chromosome Location	chr9:92791660-92791661
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	chr9:92783675..92785837-chr9:92791024..92793603,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000263967	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10820832	0.91[AFR][1000 genomes]
rs13296044	0.88[CEU][hapmap];0.83[CHB][hapmap];0.82[EUR][1000 genomes]
rs1373102	0.85[CEU][hapmap];0.83[CHB][hapmap]
rs1443360	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35150414	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs501675	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs535599	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs601472	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs613212	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs627985	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs628020	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs633926	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs636460	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs650415	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs650882	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs661232	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs666603	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs679273	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs683669	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7036231	0.89[CEU][hapmap];0.84[CHB][hapmap];0.80[EUR][1000 genomes]
rs704476	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs816526	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs920752	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893561	chr9:92732368-92802101	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
2	nsv482303	chr9:92752928-92890226	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
3	nsv614852	chr9:92786722-93100550	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:92788400-92794800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr9:92789600-92792600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr9:92789600-92806400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr9:92789800-92792200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr9:92789800-92792800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr9:92789800-92794600	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr9:92789800-92796200	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr9:92789800-92796400	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr9:92789800-92799600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr9:92790000-92792600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr9:92790000-92792800	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr9:92790000-92792800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr9:92790000-92796400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr9:92790200-92791800	Weak transcription	HMEC	breast
15	chr9:92790200-92792600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr9:92790400-92791800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr9:92791200-92793000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr9:92791600-92793200	Enhancers	NHEK	skin

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