Variant report

Variant	rs28469297
Chromosome Location	chr9:98280788-98280789
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:98279388..98282598-chr9:98285107..98287156,3	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10512247	0.81[EUR][1000 genomes]
rs10512249	0.84[CEU][hapmap];1.00[MEX][hapmap]
rs16909898	0.84[CEU][hapmap];1.00[MEX][hapmap]
rs16909902	0.84[CEU][hapmap]
rs16909923	0.82[EUR][1000 genomes]
rs16909927	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs16909930	0.82[EUR][1000 genomes]
rs16909967	0.83[EUR][1000 genomes]
rs16909981	0.89[EUR][1000 genomes]
rs1805155	1.00[MEX][hapmap]
rs2282040	0.84[CEU][hapmap];1.00[MEX][hapmap]
rs28361526	0.86[AFR][1000 genomes]
rs28372466	0.82[EUR][1000 genomes]
rs28384095	0.87[AFR][1000 genomes]
rs28446116	1.00[MEX][hapmap]
rs28520360	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs28535536	1.00[MEX][hapmap]
rs28682502	0.82[EUR][1000 genomes]
rs28698544	0.80[EUR][1000 genomes]
rs28706464	1.00[MEX][hapmap]
rs57594450	0.82[EUR][1000 genomes]
rs57594805	0.82[EUR][1000 genomes]
rs57793730	0.81[EUR][1000 genomes]
rs61076166	0.84[EUR][1000 genomes]
rs61660304	0.81[EUR][1000 genomes]
rs73529860	0.94[EUR][1000 genomes]

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	nsv531633	chr9:98078300-98431120	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv831658	chr9:98152971-98342178	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv430083	chr9:98204245-98445645	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv824994	chr9:98239963-98314431	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv824995	chr9:98243455-98326547	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv824996	chr9:98245375-98283861	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv917118	chr9:98279162-98284265	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs28469297	PTCH1	Cis_1M	lymphoblastoid	RTeQTL
rs28469297	FBP2	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98280000-98282000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr9:98280200-98281000	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr9:98280200-98281600	Enhancers	Fetal Lung	lung

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