Variant report

Variant	rs534080
Chromosome Location	chr1:57584721-57584722
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 9 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs3768171	0.84[JPT][hapmap]
rs4912428	0.80[CHB][hapmap];0.84[JPT][hapmap]
rs563670	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs564691	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs574617	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv869295	chr1:56894955-57656562	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv428752	chr1:57455083-57605082	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv461628	chr1:57463326-57816489	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv546305	chr1:57463326-57816489	Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs534080	PARS2	cis	cerebellum	SCAN
rs534080	C8B	cis	parietal	SCAN
rs534080	ACOT11	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57551400-57622000	Weak transcription	Fetal Intestine Small	intestine
2	chr1:57576200-57584800	Weak transcription	Colon Smooth Muscle	Colon
3	chr1:57577200-57595600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:57578200-57589600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:57579400-57586400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr1:57580400-57589200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr1:57583600-57593000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr1:57584400-57585000	Enhancers	Fetal Heart	heart
9	chr1:57584600-57585200	Enhancers	Fetal Lung	lung
10	chr1:57584600-57585400	Enhancers	Fetal Kidney	kidney
11	chr1:57584600-57589800	Weak transcription	NHEK	skin

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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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