Variant report

Variant	rs6573468
Chromosome Location	chr14:63453139-63453140
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:63453009..63453790-chr9:37302276..37302954,2	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1007062	0.88[CEU][hapmap];0.89[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10130015	0.89[CEU][hapmap]
rs10131734	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10132214	0.82[CEU][hapmap]
rs10132410	0.94[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap]
rs10133358	0.85[CHB][hapmap]
rs10139542	0.94[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap]
rs10142476	0.94[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10142809	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11158468	0.88[CEU][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11624884	0.86[CHB][hapmap]
rs12147350	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12589987	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12888947	0.86[ASN][1000 genomes]
rs1316916	0.83[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap]
rs1950975	0.94[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap]
rs1950986	0.89[CEU][hapmap]
rs1950990	0.94[CEU][hapmap];0.95[CHB][hapmap]
rs1956679	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2180802	0.84[CHB][hapmap]
rs28490569	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3906692	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap]
rs3906693	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs3910328	0.94[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5010674	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs5010675	0.80[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap]
rs5010676	0.82[CHB][hapmap]
rs6573475	0.88[CEU][hapmap];0.86[CHB][hapmap];0.84[JPT][hapmap]
rs67610164	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7140971	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7159483	0.94[CEU][hapmap];0.95[CHB][hapmap]
rs7160761	0.94[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.80[JPT][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap]
rs8004870	0.94[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8006836	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8011042	0.95[CHB][hapmap]
rs8018212	0.88[CEU][hapmap];0.86[CHB][hapmap]
rs9323430	0.94[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes];0.89[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	nsv527251	chr14:63400786-64068806	Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv520528	chr14:63400786-64157117	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6573468	GBX2	trans	cerebellum	SCAN
rs6573468	C14orf135	cis	parietal	SCAN

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
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