Variant report

Variant	rs9874792
Chromosome Location	chr3:55860526-55860527
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs17714443	0.84[ASN][1000 genomes]
rs4459870	0.85[ASN][1000 genomes]
rs4955882	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4955884	0.82[ASN][1000 genomes]
rs4974113	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4974147	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7615473	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9815001	0.88[CEU][hapmap];0.83[CHD][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9835091	0.88[CEU][hapmap];0.85[JPT][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9840522	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9852746	0.88[CEU][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9852888	0.88[CEU][hapmap];0.83[CHD][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9853067	0.93[CEU][hapmap];0.83[JPT][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9854025	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9854247	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9857120	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9860951	0.81[EUR][1000 genomes];0.85[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	nsv876814	chr3:55802749-55860526	Weak transcription Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv590361	chr3:55834871-55876104	Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv1013063	chr3:55835413-56173713	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
4	esv3440427	chr3:55860016-55865704	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9874792	RPL29	cis	cerebellum	SCAN
rs9874792	CCDC66	cis	parietal	SCAN
rs9874792	HESX1	cis	cerebellum	SCAN
rs9874792	TWF2	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:55860000-55861800	Enhancers	Fetal Heart	heart
2	chr3:55860200-55862200	Enhancers	Fetal Lung	lung
3	chr3:55860400-55860600	Enhancers	Brain Inferior Temporal Lobe	brain
4	chr3:55860400-55861200	Enhancers	iPS-18 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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