Variant report

Variant	rs12658881
Chromosome Location	chr5:59559145-59559146
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10434525	1.00[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1155796	1.00[YRI][hapmap]
rs11739760	0.93[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes]
rs11741663	1.00[YRI][hapmap]
rs12515974	0.83[JPT][hapmap]
rs1966497	0.93[AFR][1000 genomes]
rs2898269	1.00[YRI][hapmap]
rs2961903	1.00[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2962965	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4128924	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4700369	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56215414	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57587828	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025856	chr5:59188419-59928852	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv830316	chr5:59480269-59689829	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv4847	chr5:59523591-59569307	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59554200-59562400	Enhancers	Primary neutrophils fromperipheralblood	blood
2	chr5:59554400-59561600	Weak transcription	HepG2	liver
3	chr5:59554800-59559600	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr5:59556600-59561200	Weak transcription	Primary hematopoietic stem cells	blood
5	chr5:59557600-59559200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr5:59558400-59559600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr5:59558400-59560600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr5:59558600-59563600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr5:59558800-59559600	Enhancers	Monocytes-CD14+_RO01746	blood
10	chr5:59559000-59559600	Enhancers	Primary B cells from cord blood	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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