Variant report

Variant	rs12109479
Chromosome Location	chr5:52414583-52414584
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:52404937..52407889-chr5:52413411..52415700,2	MCF-7	breast:
2	chr5:52405040..52409450-chr5:52412330..52415161,4	K562	blood:

Variant related genes	Relation type
ENSG00000247796	Chromatin interaction
ENSG00000164172	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10940289	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2233213	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2233216	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2233220	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3212427	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3212428	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3212437	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3212454	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3212460	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3212462	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3212477	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3212534	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3212538	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3212541	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3212602	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3212608	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3212639	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3816326	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3928414	0.86[EUR][1000 genomes]
rs41308283	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7732191	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9968622	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9968673	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949005	chr5:52188028-52808229	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52406400-52419000	Weak transcription	Left Ventricle	heart
2	chr5:52406600-52414600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr5:52406800-52422000	Weak transcription	NHLF	lung
4	chr5:52406800-52422200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr5:52407000-52414800	Weak transcription	Pancreas	Pancrea
6	chr5:52407000-52418800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr5:52407000-52418800	Weak transcription	NHEK	skin
8	chr5:52407000-52419000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr5:52407200-52418800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr5:52410400-52421800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr5:52414000-52415200	Flanking Active TSS	K562	blood
12	chr5:52414000-52416000	Enhancers	Fetal Intestine Large	intestine
13	chr5:52414000-52416400	Enhancers	Fetal Intestine Small	intestine
14	chr5:52414200-52414600	Enhancers	Duodenum Mucosa	Duodenum

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