Variant report

Variant	rs2285059
Chromosome Location	chr20:23858428-23858429
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1799841	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2071443	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2071445	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4239744	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4813509	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs4815244	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6036565	0.91[EUR][1000 genomes]
rs6076157	0.95[CHB][hapmap];0.93[CHD][hapmap];0.93[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	nsv491876	chr20:23436633-24031374	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv833944	chr20:23806288-24021865	Bivalent Enhancer Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv585730	chr20:23809681-23862844	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv3411629	chr20:23855752-23860150	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer	n/a	n/a	inside rSNPs	diseases
5	nsv964382	chr20:23856148-23862860	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2285059	CST5	cis	lung	GTEx

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23848800-23860400	Enhancers	Fetal Thymus	thymus
2	chr20:23851400-23859400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr20:23852400-23864800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr20:23854800-23860600	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr20:23857400-23860600	Weak transcription	Colon Smooth Muscle	Colon
6	chr20:23858000-23858600	Enhancers	Stomach Smooth Muscle	stomach
7	chr20:23858000-23859600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr20:23858200-23858600	Bivalent Enhancer	Fetal Stomach	stomach
9	chr20:23858200-23859600	Enhancers	HMEC	breast
10	chr20:23858200-23862800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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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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