Variant report

Variant	rs12869054
Chromosome Location	chr13:76235460-76235461
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	chr13:76229874..76232136-chr13:76233228..76235959,2	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10507833	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11617360	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12427985	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12430746	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1323693	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1575478	0.93[EUR][1000 genomes]
rs1924176	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2281763	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs33991813	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34222504	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34512564	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34939695	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35915164	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61958092	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61958094	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9565180	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9573606	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9573608	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9593111	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9593112	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9593115	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9600515	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9600518	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9600521	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2751152	chr13:76144199-76288418	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv949152	chr13:76211453-76366622	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12869054	RP11-173B14.5	cis	Artery Tibial	GTEx

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:76211600-76235600	Weak transcription	Ovary	ovary
2	chr13:76211600-76235600	Weak transcription	Pancreas	Pancrea
3	chr13:76212200-76235600	Weak transcription	Aorta	Aorta
4	chr13:76212400-76240400	Weak transcription	HMEC	breast
5	chr13:76213400-76267800	Weak transcription	Primary T cells from cord blood	blood
6	chr13:76213800-76235600	Weak transcription	Psoas Muscle	Psoas
7	chr13:76215400-76258200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr13:76223200-76236600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr13:76231200-76235800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr13:76231400-76240400	Weak transcription	HSMMtube	muscle
11	chr13:76231400-76240600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr13:76231800-76240600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr13:76232400-76235800	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr13:76233800-76240600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr13:76234000-76236200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr13:76234000-76237200	Enhancers	NHDF-Ad	bronchial
17	chr13:76234000-76237200	Genic enhancers	Osteobl	bone
18	chr13:76234400-76236800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr13:76234400-76238400	Weak transcription	NH-A	brain
20	chr13:76234600-76236600	Genic enhancers	HSMM	muscle
21	chr13:76234600-76236800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr13:76234800-76236800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr13:76234800-76237200	Genic enhancers	Muscle Satellite Cultured Cells	--
24	chr13:76235200-76235600	Weak transcription	GM12878-XiMat	blood
25	chr13:76235400-76235600	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr13:76235400-76236000	Enhancers	NHLF	lung

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