Variant report

Variant	rs7839300
Chromosome Location	chr8:20950485-20950486
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10111769	0.81[ASN][1000 genomes]
rs11784441	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13250583	0.98[ASN][1000 genomes]
rs13258422	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13275050	0.87[ASN][1000 genomes]
rs13276143	0.87[ASN][1000 genomes]
rs13282584	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2013243	0.85[ASN][1000 genomes]
rs34437032	0.97[ASN][1000 genomes]
rs35256844	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35393501	0.82[ASN][1000 genomes]
rs35523999	0.94[ASN][1000 genomes]
rs35555613	0.96[ASN][1000 genomes]
rs35842344	0.88[ASN][1000 genomes]
rs35913688	0.80[ASN][1000 genomes]
rs4961390	0.87[ASN][1000 genomes]
rs59048764	0.89[ASN][1000 genomes]
rs6985275	0.86[EUR][1000 genomes];0.96[ASN][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	nsv1032450	chr8:20514995-21033577	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv539524	chr8:20514995-21033577	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1034265	chr8:20742935-21152545	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv539528	chr8:20742935-21152545	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv831260	chr8:20907266-21097125	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7839300	NKX3-1	cis	parietal	SCAN
rs7839300	LGI3	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:20946800-20951000	Enhancers	Brain Germinal Matrix	brain
2	chr8:20949000-20958200	Weak transcription	Psoas Muscle	Psoas
3	chr8:20949400-20952200	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr8:20949400-20953000	Weak transcription	Left Ventricle	heart
5	chr8:20949800-20956400	Weak transcription	Fetal Brain Male	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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