Variant report

Variant	rs17834293
Chromosome Location	chr2:142993879-142993880
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs13029758	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs13396415	1.00[CHB][hapmap]
rs1375608	1.00[CHB][hapmap]
rs1449488	0.89[CEU][hapmap]
rs1562704	0.82[TSI][hapmap]
rs17776027	0.87[EUR][1000 genomes]
rs17776043	0.87[EUR][1000 genomes]
rs17832932	0.88[EUR][1000 genomes]
rs72852610	0.83[EUR][1000 genomes]
rs72852633	0.84[EUR][1000 genomes]
rs72852654	0.87[EUR][1000 genomes]
rs72853430	0.97[EUR][1000 genomes]
rs72853432	0.97[EUR][1000 genomes]
rs7583748	0.82[TSI][hapmap]
rs7594671	0.90[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs895936	1.00[CHB][hapmap]
rs9630925	1.00[YRI][hapmap]

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	nsv997274	chr2:142760393-143599193	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1006247	chr2:142851056-143289465	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv875256	chr2:142894573-142994328	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv875257	chr2:142894573-143041082	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv459696	chr2:142972199-142998565	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv583240	chr2:142972199-142998565	Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17834293	EGR2	trans	brain	seeQTL
rs17834293	PLEK	trans	brain	seeQTL
rs17834293	PTGS2	trans	brain	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:142992400-142994600	Enhancers	Fetal Lung	lung
2	chr2:142993200-142994600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:142993400-142994200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr2:142993400-142995000	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr2:142993600-142994400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr2:142993600-142994600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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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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