Variant report

Variant	rs889829
Chromosome Location	chr5:146724726-146724727
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10041375	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10072514	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11954789	0.81[YRI][hapmap]
rs13170279	0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs17106458	0.95[LWK][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs2400294	0.81[YRI][hapmap]
rs4235730	0.96[CEU][hapmap];0.85[CHB][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4235731	0.80[CEU][hapmap];0.81[GIH][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs4705167	0.96[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6884181	0.97[LWK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs723698	0.81[EUR][1000 genomes]
rs7714559	0.81[EUR][1000 genomes]
rs9325041	0.96[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9885145	1.00[YRI][hapmap];0.91[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015804	chr5:146066000-146788233	Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv537915	chr5:146066000-146788233	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv519847	chr5:146166378-146812647	Bivalent/Poised TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv599938	chr5:146169511-146806365	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv869238	chr5:146179403-146787986	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	esv2763507	chr5:146718961-146727485	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Strong transcription Bivalent Enhancer	TF binding region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs889829	NR3C1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:146707600-146725600	Weak transcription	Pancreas	Pancrea
2	chr5:146721800-146726600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr5:146722200-146727000	Weak transcription	Aorta	Aorta
4	chr5:146723000-146727000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr5:146723000-146733400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr5:146724200-146725600	Enhancers	Primary neutrophils fromperipheralblood	blood

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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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