Variant report

Variant	rs12346151
Chromosome Location	chr9:93685729-93685730
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10124819	1.00[AMR][1000 genomes]
rs12336477	1.00[AMR][1000 genomes]
rs12345699	1.00[AMR][1000 genomes]
rs12349860	1.00[AMR][1000 genomes]
rs28476556	0.86[AFR][1000 genomes]
rs7035017	1.00[ASW][hapmap];0.91[LWK][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73492574	1.00[AMR][1000 genomes]
rs7865699	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046989	chr9:93353987-93800416	Transcr. at gene 5' and 3' Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv831652	chr9:93527411-93696923	Bivalent Enhancer Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv893568	chr9:93539879-93774385	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv1038685	chr9:93556174-93685729	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1039326	chr9:93598856-93685729	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1053252	chr9:93610132-93699103	Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12346151	RAGE	trans	lymphoblastoid	seeQTL
rs12346151	NFIL3	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:93681400-93686800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:93681400-93687200	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr9:93683000-93692000	Weak transcription	Right Ventricle	heart
4	chr9:93683800-93686200	Weak transcription	Fetal Brain Male	brain
5	chr9:93683800-93686800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr9:93683800-93687000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr9:93684000-93685800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr9:93684000-93686000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr9:93684000-93687400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr9:93684000-93687600	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr9:93684000-93688400	Weak transcription	Aorta	Aorta
12	chr9:93684200-93687800	Weak transcription	Adipose Nuclei	Adipose
13	chr9:93684600-93686200	Weak transcription	HMEC	breast
14	chr9:93684600-93687600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr9:93685600-93686200	Flanking Active TSS	GM12878-XiMat	blood
16	chr9:93685600-93687000	Enhancers	Primary B cells from peripheral blood	blood
17	chr9:93685600-93689200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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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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