Variant report

Variant	rs1823125
Chromosome Location	chr2:114090412-114090413
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:114087006..114091652-chr2:114092667..114098276,5	MCF-7	breast:

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12616641	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1807282	0.95[EUR][1000 genomes]
rs2863957	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4618068	0.95[EUR][1000 genomes]
rs56093896	0.95[EUR][1000 genomes]
rs60873293	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62158166	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62158168	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62158169	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62158170	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62158206	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62158211	0.95[EUR][1000 genomes]
rs62158213	0.95[EUR][1000 genomes]
rs6737318	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7556815	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][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	nsv508162	chr2:113983043-114099966	Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	esv2757826	chr2:114074949-114253780	Enhancers Strong transcription Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv2759085	chr2:114074949-114428678	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1823125	IL1F10	cis	parietal	SCAN
rs1823125	DPP10	cis	cerebellum	SCAN
rs1823125	AC016745.3	cis	Thyroid	GTEx

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:114083400-114090800	Weak transcription	Fetal Intestine Small	intestine
2	chr2:114083400-114108000	Weak transcription	Lung	lung
3	chr2:114087200-114092000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr2:114087600-114093600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr2:114088200-114093400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr2:114088400-114093200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr2:114088400-114093200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr2:114088400-114097600	Weak transcription	HSMM	muscle
9	chr2:114088400-114097800	Weak transcription	NH-A	brain
10	chr2:114088600-114093400	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr2:114088600-114093400	Weak transcription	NHDF-Ad	bronchial
12	chr2:114088600-114097800	Weak transcription	HSMMtube	muscle
13	chr2:114089000-114091000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr2:114089000-114097000	Weak transcription	HMEC	breast
15	chr2:114089400-114091200	Weak transcription	Right Atrium	heart
16	chr2:114089400-114093600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr2:114089600-114090600	Strong transcription	A549	lung
18	chr2:114089600-114091800	Strong transcription	NHEK	skin
19	chr2:114090200-114095400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr2:114090400-114094400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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