Variant report

Variant	rs16999299
Chromosome Location	chr20:52897256-52897257
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:52823411..52826205-chr20:52895497..52899712,3	MCF-7	breast:
2	chr10:7914281..7916763-chr20:52896829..52898926,2	MCF-7	breast:
3	chr20:52835609..52839947-chr20:52897046..52901468,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000101132	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1040857	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10485791	1.00[CHB][hapmap];0.88[CHD][hapmap];0.82[ASN][1000 genomes]
rs1157418	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1293134	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1343081	0.96[ASN][1000 genomes]
rs1477734	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1477735	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs16999320	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs16999351	1.00[CHB][hapmap];0.88[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs16999393	1.00[CHB][hapmap]
rs28372633	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28460139	0.93[ASN][1000 genomes]
rs292116	0.87[CHD][hapmap]
rs292117	0.83[CHD][hapmap]
rs292142	0.86[ASN][1000 genomes]
rs6013948	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6013954	0.81[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6013957	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6023086	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6023089	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6023092	0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6023096	0.82[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.86[LWK][hapmap];0.84[MKK][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6023105	0.91[ASN][1000 genomes]
rs6097910	1.00[CHB][hapmap]
rs7266330	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	nsv962638	chr20:52883415-52917517	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16999299	AURKA	cis	cerebellum	SCAN
rs16999299	DOK5	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52895400-52899200	Weak transcription	Fetal Brain Male	brain

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