Variant report

Variant	rs7958568
Chromosome Location	chr12:47431496-47431497
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10785649	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs10881039	0.91[EUR][1000 genomes]
rs11183677	0.84[EUR][1000 genomes]
rs11183699	0.96[CEU][hapmap];0.89[GIH][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes]
rs11183710	0.94[EUR][1000 genomes]
rs11183711	0.95[EUR][1000 genomes]
rs1989912	0.92[EUR][1000 genomes]
rs34142537	0.88[EUR][1000 genomes]
rs4768770	0.92[EUR][1000 genomes]
rs7134654	0.93[EUR][1000 genomes]
rs7305847	0.85[EUR][1000 genomes]
rs7956438	0.92[EUR][1000 genomes]
rs7960974	0.88[EUR][1000 genomes]
rs7971310	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs7971796	0.92[EUR][1000 genomes]
rs7972871	0.94[EUR][1000 genomes]
rs7978950	0.83[EUR][1000 genomes]

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	esv1845143	chr12:47051076-47431496	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv469368	chr12:47374908-47675680	Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv558784	chr12:47374908-47675680	Genic enhancers Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7958568	RAPGEF3	cis	cerebellum	SCAN
rs7958568	PFKM	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:47427800-47431800	Weak transcription	Liver	Liver
2	chr12:47428600-47431800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr12:47428800-47433000	Weak transcription	Osteobl	bone
4	chr12:47429200-47433800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr12:47429400-47450000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr12:47429800-47433800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr12:47430800-47432600	Enhancers	Fetal Intestine Large	intestine
8	chr12:47431000-47431600	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr12:47431000-47433200	Enhancers	Fetal Intestine Small	intestine
10	chr12:47431200-47432000	Flanking Active TSS	A549	lung
11	chr12:47431400-47431600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr12:47431400-47432000	Enhancers	Rectal Mucosa Donor 29	rectum

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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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