Variant report

Variant	rs12555122
Chromosome Location	chr9:102151801-102151802
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:102142513..102144280-chr9:102150068..102152922,2	MCF-7	breast:

Extended variants
information (count: 9 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10988808	0.85[AMR][1000 genomes]
rs188940	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs421723	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56305307	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67121785	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9886848	0.83[CEU][hapmap];0.88[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893620	chr9:102029791-102194921	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv831667	chr9:102068047-102285691	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1046898	chr9:102111890-102163313	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	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
rs12555122	ERP44	cis	cerebellum	SCAN
rs12555122	NR4A3	cis	parietal	SCAN
rs12555122	FBP2	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:102148400-102154200	Weak transcription	Left Ventricle	heart
2	chr9:102148400-102161800	Weak transcription	Right Ventricle	heart
3	chr9:102148600-102153800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr9:102151000-102152000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr9:102151000-102152200	Enhancers	HMEC	breast
6	chr9:102151200-102152000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr9:102151200-102152200	Enhancers	NHEK	skin
8	chr9:102151400-102152000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr9:102151400-102152000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr9:102151400-102152000	Enhancers	Placenta	Placenta
11	chr9:102151400-102152000	Enhancers	Right Atrium	heart
12	chr9:102151400-102152200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr9:102151400-102152200	Enhancers	NH-A	brain
14	chr9:102151400-102152200	Enhancers	NHDF-Ad	bronchial
15	chr9:102151400-102152400	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr9:102151600-102152000	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr9:102151600-102152000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr9:102151600-102152000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr9:102151600-102152000	Enhancers	HUVEC	blood vessel
20	chr9:102151600-102152200	Enhancers	K562	blood
21	chr9:102151800-102152000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr9:102151800-102159000	Weak transcription	NHLF	lung

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