Variant report

Variant	rs4977445
Chromosome Location	chr9:18806500-18806501
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs4977446	0.87[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.96[YRI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4977448	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6475247	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.86[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	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	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
8	nsv949111	chr9:18758205-18994588	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4977445	DCTN3	trans	cerebellum	SCAN
rs4977445	HMGB1	trans	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:18778400-18817000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:18788000-18825200	Weak transcription	HUVEC	blood vessel
3	chr9:18796800-18817400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr9:18798800-18811200	Weak transcription	Aorta	Aorta
5	chr9:18800000-18824200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr9:18801200-18809000	Strong transcription	HSMM	muscle
7	chr9:18801200-18817600	Weak transcription	HSMMtube	muscle
8	chr9:18802000-18811400	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr9:18802200-18806600	Weak transcription	Fetal Stomach	stomach
10	chr9:18802200-18811200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr9:18802400-18817000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr9:18803200-18817000	Weak transcription	NH-A	brain
13	chr9:18804800-18809400	Strong transcription	Osteobl	bone
14	chr9:18805400-18807200	Enhancers	Stomach Smooth Muscle	stomach
15	chr9:18805800-18807000	Enhancers	Pancreatic Islets	Pancreatic Islet
16	chr9:18805800-18807600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr9:18805800-18808400	Strong transcription	NHDF-Ad	bronchial
18	chr9:18806000-18806800	Enhancers	HepG2	liver
19	chr9:18806000-18809000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr9:18806200-18806600	Enhancers	Colon Smooth Muscle	Colon
21	chr9:18806200-18807200	Enhancers	Fetal Lung	lung
22	chr9:18806400-18807000	Enhancers	Fetal Muscle Leg	muscle
23	chr9:18806400-18826000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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