Variant report

Variant	rs62571050
Chromosome Location	chr9:15540604-15540605
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr9:15540310-15540809	MCF-7	breast:	n/a	n/a
2	GATA3	chr9:15540145-15540942	MCF-7	breast:	n/a	n/a
3	MAFK	chr9:15540577-15540859	HepG2	liver:	n/a	n/a
4	GATA3	chr9:15540440-15540777	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:15540367..15542446-chr9:15551493..15554062,3	MCF-7	breast:

Variant related genes	Relation type
RNU6-246P	TF binding region
ENSG00000164989	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs16933350	0.87[EUR][1000 genomes]
rs3087653	0.83[EUR][1000 genomes]
rs41268961	0.83[EUR][1000 genomes]
rs41306098	0.83[EUR][1000 genomes]
rs59355275	0.92[EUR][1000 genomes]
rs59520337	0.87[EUR][1000 genomes]
rs62570980	0.83[EUR][1000 genomes]
rs62570991	0.83[EUR][1000 genomes]
rs62570992	0.83[EUR][1000 genomes]
rs62570993	0.83[EUR][1000 genomes]
rs62571003	0.80[EUR][1000 genomes]
rs62571007	0.83[EUR][1000 genomes]
rs62571008	0.80[EUR][1000 genomes]
rs62571009	0.83[EUR][1000 genomes]
rs62571011	0.83[EUR][1000 genomes]
rs62571015	0.92[EUR][1000 genomes]
rs62571016	0.92[EUR][1000 genomes]
rs62571017	0.92[EUR][1000 genomes]
rs62571018	0.87[EUR][1000 genomes]
rs62571029	0.87[EUR][1000 genomes]
rs62571033	0.92[EUR][1000 genomes]
rs62571037	0.95[EUR][1000 genomes]
rs62571046	0.92[EUR][1000 genomes]
rs62571047	0.92[EUR][1000 genomes]
rs62571048	0.92[EUR][1000 genomes]
rs62571051	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62571052	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7856523	0.92[EUR][1000 genomes]
rs7856657	0.90[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	nsv892625	chr9:15326251-16064850	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv892626	chr9:15389610-15694690	Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv892627	chr9:15397969-15909450	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv892629	chr9:15516375-15634326	Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	esv3407839	chr9:15530438-15665653	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62571050	PSIP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:0 , 50 per page) page:

No data

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