Variant report

Variant	rs2238280
Chromosome Location	chr14:72425522-72425523
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	chr14:72400385..72403304-chr14:72425307..72428044,2	MCF-7	breast:
2	chr14:72423860..72426368-chr14:72427413..72429540,3	MCF-7	breast:

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1009017	0.95[CEU][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];0.84[MEX][hapmap];0.82[EUR][1000 genomes]
rs11158920	0.93[CHB][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs11158921	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11158927	0.87[CHB][hapmap];0.89[CHD][hapmap]
rs11620690	0.93[CHB][hapmap]
rs11623376	0.87[CEU][hapmap]
rs11623492	0.93[CHB][hapmap];0.89[CHD][hapmap];0.84[MEX][hapmap]
rs11623535	0.91[CEU][hapmap];0.93[CHB][hapmap];0.89[CHD][hapmap];0.90[MEX][hapmap];0.82[EUR][1000 genomes]
rs11625937	0.93[CHB][hapmap];0.89[CHD][hapmap];0.89[MEX][hapmap]
rs11627768	0.92[CHB][hapmap];0.86[JPT][hapmap]
rs11628133	0.81[CHB][hapmap]
rs12148043	0.87[CHB][hapmap];0.82[CHD][hapmap]
rs12433721	0.93[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs12437172	0.91[ASN][1000 genomes]
rs12883063	0.91[CEU][hapmap]
rs12884202	0.83[CEU][hapmap]
rs12884483	0.83[CEU][hapmap]
rs12885938	0.83[CEU][hapmap]
rs12897386	0.91[CEU][hapmap]
rs12897929	0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs17093750	0.87[CHB][hapmap]
rs17105346	0.93[CHB][hapmap];0.89[CHD][hapmap];0.89[MEX][hapmap]
rs17105566	0.93[CHB][hapmap]
rs17105606	0.87[CHB][hapmap]
rs17105690	0.85[CHB][hapmap]
rs1987722	0.82[EUR][1000 genomes]
rs1987723	0.84[EUR][1000 genomes]
rs2010846	0.84[EUR][1000 genomes]
rs2010850	0.82[EUR][1000 genomes]
rs2067856	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2159457	0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2215132	0.82[CEU][hapmap]
rs2238268	0.87[CEU][hapmap]
rs2238277	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[JPT][hapmap];0.91[ASN][1000 genomes]
rs2239267	0.83[CEU][hapmap]
rs2239268	0.83[CEU][hapmap]
rs3784055	0.93[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap];0.83[ASN][1000 genomes]
rs3784056	0.93[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap];0.84[ASN][1000 genomes]
rs3784058	0.93[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs4048388	0.91[CEU][hapmap]
rs4243640	0.91[CEU][hapmap];0.93[CHB][hapmap];0.89[CHD][hapmap];0.85[MEX][hapmap];0.82[EUR][1000 genomes]
rs4350510	0.91[CEU][hapmap];0.93[CHB][hapmap];0.82[EUR][1000 genomes]
rs4354860	0.91[CEU][hapmap];0.93[CHB][hapmap];0.89[CHD][hapmap];0.90[MEX][hapmap];0.82[EUR][1000 genomes]
rs4899409	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4899412	0.86[CEU][hapmap];0.93[CHB][hapmap];0.89[CHD][hapmap];0.89[MEX][hapmap]
rs4902958	1.00[CHB][hapmap];0.82[JPT][hapmap];0.94[ASN][1000 genomes]
rs4902966	0.91[CEU][hapmap];0.93[CHB][hapmap];0.82[EUR][1000 genomes]
rs56067914	0.83[ASN][1000 genomes]
rs56743778	0.82[ASN][1000 genomes]
rs6574037	0.91[CEU][hapmap]
rs699358	0.83[EUR][1000 genomes]
rs72734102	0.94[ASN][1000 genomes]
rs72735921	0.94[ASN][1000 genomes]
rs72735923	0.94[ASN][1000 genomes]
rs728497	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7493353	0.89[ASN][1000 genomes]
rs8008678	0.91[CEU][hapmap]
rs8013467	0.95[CEU][hapmap];0.93[CHB][hapmap];0.89[CHD][hapmap];0.95[MEX][hapmap];0.83[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530794	chr14:72113818-73034008	Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2238280	PCNX	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:72425200-72425600	Enhancers	Cortex derived primary cultured neurospheres	brain
2	chr14:72425200-72425600	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr14:72425400-72425600	Enhancers	Left Ventricle	heart
4	chr14:72425400-72427000	Enhancers	Adipose Nuclei	Adipose
5	chr14:72425400-72427800	Weak transcription	GM12878-XiMat	blood

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