Variant report

Variant	rs10746688
Chromosome Location	chr9:85350368-85350369
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11139718	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11139719	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11139720	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12683452	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs479375	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs534724	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs556689	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs581711	0.80[EUR][1000 genomes]
rs583597	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs595666	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs599817	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs609444	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs635714	0.83[EUR][1000 genomes]
rs6559681	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7047996	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7869543	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10746688	PSAT1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:85346000-85351400	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr9:85347200-85352200	Enhancers	HUES6 Cell Line	embryonic stem cell
3	chr9:85347200-85353000	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr9:85347600-85353400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr9:85348200-85361400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr9:85349000-85351600	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr9:85349000-85352400	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr9:85349200-85350400	Enhancers	iPS-20b Cell Line	embryonic stem cell
9	chr9:85349400-85352400	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr9:85349400-85352400	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr9:85349800-85361600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr9:85350000-85364600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr9:85350200-85350400	Flanking Active TSS	ES-WA7 Cell Line	embryonic stem cell

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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