Variant report

Variant	rs1584468
Chromosome Location	chr5:119937691-119937692
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1037566	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12515727	1.00[MEX][hapmap]
rs1375462	0.83[YRI][hapmap]
rs1449168	1.00[MEX][hapmap]
rs1584463	0.91[AFR][1000 genomes]
rs1584464	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1584465	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1597285	1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs1851931	0.89[LWK][hapmap];0.87[YRI][hapmap]
rs1997004	1.00[CEU][hapmap];0.87[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2085179	0.83[AFR][1000 genomes]
rs2167022	1.00[MEX][hapmap]
rs35879493	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4895267	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4895269	1.00[MEX][hapmap]
rs6595243	0.85[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7711209	1.00[CEU][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9717027	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]

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	nsv532200	chr5:119317901-120102513	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv830463	chr5:119806643-119968825	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1031453	chr5:119843593-120393038	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv948613	chr5:119861955-119999008	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv599602	chr5:119866504-120023393	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv949499	chr5:119869763-119999008	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Immune reponse to smallpox (secreted IL-12p40)	22610502	GWAS catalog

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:119935600-119938600	Weak transcription	NHDF-Ad	bronchial
2	chr5:119935600-119940200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr5:119935800-119939600	Weak transcription	HSMM	muscle
4	chr5:119935800-119940000	Weak transcription	NHLF	lung
5	chr5:119935800-119940200	Weak transcription	Hela-S3	cervix
6	chr5:119936000-119938200	Weak transcription	Osteobl	bone
7	chr5:119936600-119938200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr5:119936600-119940000	Weak transcription	HMEC	breast
9	chr5:119937600-119938400	Enhancers	Muscle Satellite Cultured Cells	--

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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