Variant report

Variant	rs11742124
Chromosome Location	chr5:2014989-2014990
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:2013280..2015033-chr5:2015191..2017908,2	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11739768	0.84[EUR][1000 genomes]
rs11742050	0.84[EUR][1000 genomes]
rs11742732	0.84[EUR][1000 genomes]
rs11743335	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs11743444	0.84[EUR][1000 genomes]
rs11743517	0.84[EUR][1000 genomes]
rs11743549	0.84[EUR][1000 genomes]
rs11746472	0.84[EUR][1000 genomes]
rs11747860	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17539841	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.91[TSI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2035612	0.84[EUR][1000 genomes]
rs28608609	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3950476	0.80[CEU][hapmap];0.84[EUR][1000 genomes]
rs56144523	0.84[EUR][1000 genomes]
rs62337139	0.83[EUR][1000 genomes]
rs62338660	0.84[EUR][1000 genomes]
rs62338665	0.84[EUR][1000 genomes]
rs62338677	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62338679	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6860447	0.82[CEU][hapmap];0.94[GIH][hapmap];0.84[EUR][1000 genomes]
rs6860916	0.83[EUR][1000 genomes]
rs7725117	0.84[EUR][1000 genomes]
rs7726401	0.84[EUR][1000 genomes]
rs7726409	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817407	chr5:1495354-2191460	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	107 gene(s)	inside rSNPs	diseases
2	nsv869236	chr5:1719263-2259100	Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
3	nsv915846	chr5:1891098-2167677	Active TSS Genic enhancers Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1026930	chr5:1898993-2126061	Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv427705	chr5:1950467-2115059	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11742124	BRD9	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:2012600-2015200	Enhancers	Fetal Heart	heart
2	chr5:2012800-2015200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr5:2013200-2015600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr5:2013800-2018800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr5:2014000-2015200	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr5:2014000-2020200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr5:2014400-2015000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr5:2014800-2025000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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