Variant report

Variant	rs727409
Chromosome Location	chr20:24557527-24557528
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs13039850	0.91[CHB][hapmap];0.93[CHD][hapmap];0.83[MEX][hapmap]
rs1409371	0.80[CHD][hapmap]
rs1980821	0.82[CEU][hapmap];0.91[CHB][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1980822	0.90[CHB][hapmap];0.82[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35191387	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4815278	0.82[CHD][hapmap]
rs4815279	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6076237	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6083555	0.82[CEU][hapmap];0.91[CHB][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6083556	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6083558	0.80[CHD][hapmap]
rs6083562	0.80[CHD][hapmap]
rs6138330	0.80[CHD][hapmap]
rs8126241	0.90[CHB][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv9793	chr20:23939613-24734850	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	esv3332519	chr20:24535099-24815615	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs727409	GZF1	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24538800-24570200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr20:24549800-24565800	Weak transcription	Thymus	Thymus
3	chr20:24552000-24562200	Weak transcription	Right Ventricle	heart
4	chr20:24553800-24564800	Weak transcription	Brain Anterior Caudate	brain
5	chr20:24554000-24560400	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr20:24554000-24564800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr20:24554600-24560400	Weak transcription	Brain Angular Gyrus	brain
8	chr20:24554600-24562000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr20:24555800-24564000	Weak transcription	Brain Hippocampus Middle	brain
10	chr20:24556000-24560200	Weak transcription	Brain Substantia Nigra	brain

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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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