Variant report

Variant	rs534724
Chromosome Location	chr9:85342969-85342970
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	chr9:85337489..85340420-chr9:85340684..85343232,2	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10746688	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11139718	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11139719	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11139720	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12683452	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs472867	0.83[AMR][1000 genomes]
rs477678	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs479375	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs485522	0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs487454	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs502630	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs503589	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs504407	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs509053	0.81[AMR][1000 genomes]
rs516033	0.82[AMR][1000 genomes]
rs518662	0.81[AMR][1000 genomes]
rs531845	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs536317	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs555869	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs556689	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs564058	0.98[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs581711	0.81[EUR][1000 genomes]
rs583597	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs595666	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs599817	0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs609444	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs635714	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6559681	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs7047996	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7869543	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428539	chr9:85240027-85402367	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs534724	PSAT1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:85331800-85345000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr9:85336000-85344800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr9:85336400-85344600	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr9:85337200-85344800	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr9:85337400-85344800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr9:85337400-85345000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr9:85340200-85344800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr9:85342000-85347400	Weak transcription	Dnd41	blood

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