Variant report

Variant	rs12000417
Chromosome Location	chr9:118452478-118452479
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs2157672	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56364993	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58053524	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs59229212	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62575352	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62575356	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62575357	0.84[EUR][1000 genomes]
rs62577060	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7025537	0.84[EUR][1000 genomes]
rs7045256	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73517508	0.84[EUR][1000 genomes]
rs73654588	1.00[ASN][1000 genomes]
rs7866856	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7869007	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs982463	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs982464	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv615251	chr9:117975864-118514444	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv948346	chr9:118107565-118718197	Enhancers Bivalent Enhancer Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1046948	chr9:118185587-118926891	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv916622	chr9:118206309-118952390	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv540207	chr9:118206311-118920304	Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv491661	chr9:118206312-118802177	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv1047164	chr9:118286742-118456851	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:118439600-118453200	Weak transcription	HSMM	muscle
2	chr9:118442400-118452800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr9:118449800-118452800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr9:118450000-118452800	Weak transcription	HMEC	breast
5	chr9:118450000-118453000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr9:118451000-118453000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr9:118451000-118455200	Enhancers	Hela-S3	cervix
8	chr9:118451200-118453600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr9:118451800-118452800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr9:118452200-118452600	Weak transcription	NHDF-Ad	bronchial
11	chr9:118452400-118453000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr9:118452400-118453000	Weak transcription	A549	lung
13	chr9:118452400-118454200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr9:118452400-118454800	Enhancers	NHEK	skin

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dbSNP/dbVar ID: rs12345 /nsv7879
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