Variant report

Variant	rs16936281
Chromosome Location	chr9:18058912-18058913
allele	C/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:15)

rs_ID	r²[population]
rs1411247	1.00[ASN][1000 genomes]
rs2776660	1.00[ASN][1000 genomes]
rs58623352	1.00[EUR][1000 genomes]
rs62548502	1.00[ASN][1000 genomes]
rs62548504	0.84[EUR][1000 genomes]
rs62549860	0.82[EUR][1000 genomes]
rs66516931	1.00[EUR][1000 genomes]
rs66807314	0.97[EUR][1000 genomes]
rs67734151	0.92[EUR][1000 genomes]
rs72697461	1.00[EUR][1000 genomes]
rs72697469	0.95[EUR][1000 genomes]
rs73643490	1.00[ASN][1000 genomes]
rs73643495	1.00[ASN][1000 genomes]
rs7849523	0.97[EUR][1000 genomes]
rs7864879	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv613706	chr9:17718918-18090934	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv613707	chr9:17720175-18070475	Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv613708	chr9:17720175-18072085	Enhancers Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv1021605	chr9:18002205-18271109	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv892678	chr9:18033944-18082567	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv466280	chr9:18033944-18166112	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv471288	chr9:18033944-18166112	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv613723	chr9:18033944-18166112	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv892679	chr9:18044802-18226609	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16936281	VIM	trans	lymphoblastoid	seeQTL

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:18038400-18061600	Weak transcription	Aorta	Aorta
2	chr9:18056000-18059400	Enhancers	Primary hematopoietic stem cells short term culture	blood
3	chr9:18057200-18059000	Weak transcription	Colon Smooth Muscle	Colon
4	chr9:18057200-18059000	Weak transcription	Ovary	ovary
5	chr9:18057200-18059000	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr9:18057800-18059000	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr9:18058000-18059800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr9:18058200-18059200	Enhancers	Fetal Intestine Small	intestine
9	chr9:18058600-18059200	Enhancers	Fetal Intestine Large	intestine
10	chr9:18058800-18059000	Enhancers	Duodenum Smooth Muscle	Duodenum
11	chr9:18058800-18059200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr9:18058800-18059200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr9:18058800-18059200	Enhancers	Fetal Lung	lung
14	chr9:18058800-18059200	Enhancers	Stomach Mucosa	stomach
15	chr9:18058800-18059400	Enhancers	Small Intestine	intestine

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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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