Variant report

Variant	rs6554881
Chromosome Location	chr5:15392590-15392591
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11955129	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs304540	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs304553	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs304585	1.00[AMR][1000 genomes]
rs304588	1.00[AMR][1000 genomes]
rs524928	1.00[AMR][1000 genomes]
rs566631	1.00[AMR][1000 genomes]
rs590066	1.00[AMR][1000 genomes]
rs592200	1.00[AMR][1000 genomes]
rs599166	1.00[ASW][hapmap];0.81[LWK][hapmap];1.00[AMR][1000 genomes]
rs626130	1.00[AMR][1000 genomes]
rs641200	1.00[AMR][1000 genomes]
rs644859	1.00[AMR][1000 genomes]
rs6554879	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs667260	1.00[AMR][1000 genomes]
rs670272	1.00[AMR][1000 genomes]
rs676820	1.00[AMR][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	nsv516929	chr5:15087791-15870300	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1023068	chr5:15095221-15863583	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv869040	chr5:15097602-15866117	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv530222	chr5:15151662-15851485	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv881558	chr5:15291398-15420775	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6554881	RNF128	trans	lymphoblastoid	seeQTL

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:15391600-15392600	Enhancers	HUES48 Cell Line	embryonic stem cell
2	chr5:15391800-15392600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr5:15391800-15392600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr5:15392000-15392600	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr5:15392000-15392600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr5:15392000-15392600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr5:15392000-15392600	Enhancers	Adipose Nuclei	Adipose
8	chr5:15392200-15392600	Active TSS	NHDF-Ad	bronchial
9	chr5:15392400-15392800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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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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