Variant report

Variant	rs1539000
Chromosome Location	chr9:18602403-18602404
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10810993	0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10810994	0.95[ASN][1000 genomes]
rs11532901	0.89[JPT][hapmap]
rs12684130	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs1412673	0.86[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap]
rs16936905	0.82[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.95[LWK][hapmap];0.81[ASN][1000 genomes]
rs16936917	0.82[CHB][hapmap]
rs1889006	0.81[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs7867475	0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491807	chr9:18243672-19009770	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv525659	chr9:18288212-19009041	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1019127	chr9:18288271-18996288	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv1029449	chr9:18414752-18829127	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
5	nsv540077	chr9:18414752-18829127	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
6	nsv1030931	chr9:18414752-18903530	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv428536	chr9:18512807-18667760	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
8	nsv892691	chr9:18519699-18805483	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
9	nsv892692	chr9:18519699-19045502	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
10	nsv6496	chr9:18586934-18609801	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS	n/a	n/a	inside rSNPs	diseases
11	nsv831523	chr9:18592398-18753451	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
12	nsv892694	chr9:18599029-18767830	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1539000	CER1	cis	parietal	SCAN
rs1539000	C15orf44	trans	cerebellum	SCAN
rs1539000	BNC2	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:18584000-18603200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr9:18588600-18605600	Weak transcription	NH-A	brain
3	chr9:18592600-18605800	Weak transcription	Aorta	Aorta
4	chr9:18594200-18605800	Weak transcription	HSMMtube	muscle
5	chr9:18595800-18604600	Weak transcription	Fetal Stomach	stomach
6	chr9:18596000-18605800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr9:18598000-18603200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr9:18598000-18605200	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr9:18599400-18604600	Weak transcription	Brain Germinal Matrix	brain
10	chr9:18601600-18605200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr9:18601800-18604800	Weak transcription	Liver	Liver
12	chr9:18602000-18602600	Enhancers	Fetal Kidney	kidney
13	chr9:18602000-18603200	Strong transcription	HSMM	muscle
14	chr9:18602200-18603000	Weak transcription	Osteobl	bone
15	chr9:18602200-18604400	Strong transcription	Muscle Satellite Cultured Cells	--
16	chr9:18602400-18602600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr9:18602400-18602800	Genic enhancers	NHDF-Ad	bronchial
18	chr9:18602400-18603400	Weak transcription	Fetal Heart	heart

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dbSNP/dbVar ID: rs12345 /nsv7879
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