Variant report

Variant	rs6559679
Chromosome Location	chr9:85353141-85353142
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10746687	0.81[EUR][1000 genomes]
rs10867866	0.81[EUR][1000 genomes]
rs10867867	0.80[EUR][1000 genomes]
rs10867868	0.81[EUR][1000 genomes]
rs11139684	0.80[EUR][1000 genomes]
rs11139688	0.80[EUR][1000 genomes]
rs1332471	0.81[EUR][1000 genomes]
rs472867	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs477678	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs485522	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs487454	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4877702	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4877703	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4877704	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs493701	0.85[EUR][1000 genomes]
rs502630	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs503589	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs504407	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs509053	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs509091	0.92[EUR][1000 genomes]
rs514224	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs514471	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs516033	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs518662	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs531845	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs533106	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs536317	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs540014	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs555869	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs564058	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs574896	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs574979	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs581711	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs581729	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs617565	0.84[EUR][1000 genomes]
rs682894	0.84[EUR][1000 genomes]
rs7043569	0.94[ASN][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	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
2	nsv1035314	chr9:85348780-85549246	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv540161	chr9:85348780-85549246	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1039930	chr9:85349993-85536746	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	esv1002297	chr9:85351450-85360245	Enhancers Weak transcription Genic enhancers Strong transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6559679	PSAT1	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:85347600-85353400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr9:85348200-85361400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr9:85349800-85361600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr9:85350000-85364600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr9:85351000-85356000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr9:85352200-85361200	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr9:85352200-85364800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr9:85352400-85354800	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr9:85352400-85355600	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr9:85352400-85361600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr9:85353000-85353200	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr9:85353000-85355200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr9:85353000-85361600	Strong transcription	ES-I3 Cell Line	embryonic stem cell

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