Variant report

Variant	rs2585417
Chromosome Location	chr20:52843799-52843800
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1418925	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.85[JPT][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2585418	0.91[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs292113	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs292118	0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs292119	0.83[ASN][1000 genomes]
rs3479	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs368933	0.91[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs391235	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs422066	0.88[EUR][1000 genomes]
rs422257	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs441506	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs51301	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6013925	1.00[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6013938	0.89[ASN][1000 genomes]
rs6091837	0.97[ASN][1000 genomes]
rs6123368	0.85[ASN][1000 genomes]
rs6127138	1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[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	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

Variant related diseases (count:1)

Disease	PMID	Source
Obesity-related traits	23251661	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2585417	AURKA	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52829400-52847400	Weak transcription	Aorta	Aorta
2	chr20:52829600-52847600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr20:52833000-52845400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr20:52834600-52845200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr20:52834600-52845200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr20:52834600-52845200	Weak transcription	NHEK	skin
7	chr20:52835600-52845800	Weak transcription	HSMM	muscle
8	chr20:52835600-52846000	Weak transcription	HSMMtube	muscle
9	chr20:52838600-52846000	Weak transcription	Fetal Muscle Leg	muscle
10	chr20:52839200-52843800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr20:52839600-52845400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr20:52840600-52849000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr20:52840800-52849000	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr20:52841000-52851000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr20:52843600-52844000	Enhancers	Primary B cells from peripheral blood	blood
16	chr20:52843600-52844600	Enhancers	GM12878-XiMat	blood

Quick Search:

Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

what's new

Quick links