Variant report

Variant	rs6827713
Chromosome Location	chr4:79936878-79936879
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10049916	1.00[JPT][hapmap]
rs10518207	1.00[JPT][hapmap]
rs1351418	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1564462	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17003468	1.00[MEX][hapmap]
rs1871707	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs286475	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs286481	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28780400	0.80[AFR][1000 genomes]
rs3925534	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6534103	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6846192	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs6855861	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs7695373	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs899901	1.00[AFR][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	nsv829979	chr4:79819168-80019159	Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv1000907	chr4:79838948-80224764	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv879505	chr4:79887043-80293046	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv3448470	chr4:79898340-80026510	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv432614	chr4:79910989-79993822	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6827713	PTGS2	trans	brain	seeQTL
rs6827713	CCL4	trans	brain	seeQTL
rs6827713	EGR4	trans	brain	seeQTL
rs6827713	GADD45G	trans	brain	seeQTL
rs6827713	FOSB	trans	brain	seeQTL
rs6827713	FOS	trans	brain	seeQTL
rs6827713	EGR2	trans	brain	seeQTL

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79936600-79937000	Enhancers	Brain Substantia Nigra	brain
2	chr4:79936800-79937200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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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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