Variant report

Variant	rs9394492
Chromosome Location	chr6:38332610-38332611
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1883610	0.96[CEU][hapmap];0.89[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap]
rs4711542	0.88[CHD][hapmap]
rs4711546	0.88[CHD][hapmap]
rs4714152	0.88[CHD][hapmap]
rs6901086	0.88[CHD][hapmap]
rs6904723	0.88[CHD][hapmap]
rs7748599	0.88[CHD][hapmap]
rs9349073	0.88[CHD][hapmap]
rs9380739	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv534620	chr6:38049585-38602064	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv885818	chr6:38147745-38436317	Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv885820	chr6:38166511-38468887	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv602957	chr6:38305770-38395874	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv1032358	chr6:38323745-38415855	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv1022724	chr6:38332368-38454527	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9394492	GLO1	cis	parietal	SCAN
rs9394492	CPNE5	cis	parietal	SCAN
rs9394492	GLO1	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38315800-38339000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:38319200-38334200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr6:38326200-38338600	Weak transcription	Ovary	ovary
4	chr6:38326400-38337200	Weak transcription	Psoas Muscle	Psoas
5	chr6:38327400-38338600	Weak transcription	Left Ventricle	heart
6	chr6:38330000-38338000	Weak transcription	Fetal Kidney	kidney
7	chr6:38331200-38333200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr6:38331200-38333200	Enhancers	NHDF-Ad	bronchial
9	chr6:38331200-38339000	Weak transcription	Right Atrium	heart
10	chr6:38331400-38332800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr6:38331400-38332800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr6:38331800-38332800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr6:38332200-38337800	Weak transcription	Adipose Nuclei	Adipose
14	chr6:38332400-38333200	Enhancers	HSMMtube	muscle
15	chr6:38332400-38333400	Enhancers	Skeletal Muscle Male	skeletal muscle
16	chr6:38332600-38332800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr6:38332600-38333000	Enhancers	NHEK	skin

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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