Variant report

Variant	rs292123
Chromosome Location	chr20:52872692-52872693
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:52852456..52856671-chr20:52869199..52873917,7	MCF-7	breast:
2	chr20:52700468..52702286-chr20:52872421..52874639,2	MCF-7	breast:
3	chr20:52827870..52830545-chr20:52871348..52873782,2	MCF-7	breast:
4	chr20:52870852..52872943-chr3:64020016..64022874,4	MCF-7	breast:
5	chr20:52823499..52826425-chr20:52871011..52873800,2	MCF-7	breast:
6	chr20:52870717..52873614-chr20:52960428..52962256,2	MCF-7	breast:
7	chr1:155055878..155058411-chr20:52870566..52873238,2	MCF-7	breast:
8	chr20:52830936..52833739-chr20:52871496..52873804,2	MCF-7	breast:
9	chr20:52872209..52873824-chr20:52943616..52946580,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000143590	Chromatin interaction
ENSG00000101132	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1293132	0.96[CEU][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1293144	0.89[CEU][hapmap];0.88[MEX][hapmap]
rs1298513	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1382015	0.88[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs1477730	0.91[ASN][1000 genomes]
rs1542523	0.82[EUR][1000 genomes]
rs2061721	0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs2153964	0.81[EUR][1000 genomes]
rs2153965	0.81[EUR][1000 genomes]
rs2185849	0.83[EUR][1000 genomes]
rs2585418	0.92[MKK][hapmap]
rs2616330	0.82[EUR][1000 genomes]
rs2616335	0.81[EUR][1000 genomes]
rs292120	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs292125	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs292126	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs292132	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs292139	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs292141	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs292143	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs292144	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs292146	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs368933	0.83[CEU][hapmap]
rs6013944	0.89[CEU][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6023082	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6127152	0.81[GIH][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	nsv586224	chr20:52474850-53279490	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	338 gene(s)	inside rSNPs	diseases
2	nsv834010	chr20:52759824-52932939	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
3	nsv834011	chr20:52858341-53086042	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs292123	AURKA	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52870600-52874400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr20:52870800-52874200	Enhancers	Muscle Satellite Cultured Cells	--
3	chr20:52870800-52874400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr20:52871000-52875000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr20:52871000-52875000	Enhancers	HMEC	breast
6	chr20:52871000-52875400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr20:52871200-52874200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr20:52871200-52875000	Enhancers	NHEK	skin
9	chr20:52871400-52874200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr20:52871400-52874400	Enhancers	Hela-S3	cervix
11	chr20:52871400-52874400	Enhancers	Osteobl	bone
12	chr20:52871400-52875000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr20:52871800-52874000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr20:52871800-52874000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr20:52871800-52874200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr20:52872000-52874200	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr20:52872200-52873000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr20:52872200-52873000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr20:52872200-52874400	Enhancers	NH-A	brain
20	chr20:52872400-52875000	Enhancers	Placenta Amnion	Placenta Amnion
21	chr20:52872600-52872800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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