Variant report

Variant	rs9568523
Chromosome Location	chr13:51692159-51692160
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1328359	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2408332	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4942950	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6561612	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9316519	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9563025	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568519	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9568529	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs957434	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832610	chr13:51636661-51822106	Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	esv3324704	chr13:51690951-51695249	Weak transcription Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
3	esv3346344	chr13:51691751-51694849	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9568523	GUCY1B2	cis	parietal	SCAN
rs9568523	GUCY1B2	cis	Skin Sun Exposed Lower leg	GTEx
rs9568523	GUCY1B2	cis	lung	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:51672800-51692400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr13:51676200-51695200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr13:51686000-51693000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr13:51690000-51697000	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr13:51691000-51693200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr13:51691800-51697400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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

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