Variant report

Variant	rs12883063
Chromosome Location	chr14:72473230-72473231
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	chr14:72468951..72470945-chr14:72473114..72474877,2	MCF-7	breast:
2	chr14:72471348..72475296-chr14:72476061..72479631,3	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1009017	0.95[CEU][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes]
rs11623376	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11623535	1.00[CEU][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes]
rs12586947	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12586968	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12884202	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12884483	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12885938	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12892100	0.86[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs12897386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1987722	0.88[EUR][1000 genomes]
rs1987723	0.87[EUR][1000 genomes]
rs2010846	0.87[EUR][1000 genomes]
rs2010850	0.88[EUR][1000 genomes]
rs2190867	0.81[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.85[ASN][1000 genomes]
rs2215132	0.91[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2238268	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2238269	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2238270	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2238272	0.83[CHB][hapmap];0.81[CHD][hapmap]
rs2238280	0.91[CEU][hapmap]
rs2239267	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2239268	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2332707	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35727014	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4048388	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4243640	1.00[CEU][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes]
rs4350510	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs4354860	1.00[CEU][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes]
rs4899412	0.95[CEU][hapmap]
rs4902966	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs6574037	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6574038	0.86[ASN][1000 genomes]
rs699358	0.88[EUR][1000 genomes]
rs8008678	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8013467	0.95[CEU][hapmap];0.92[TSI][hapmap];0.88[EUR][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	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
2	nsv948800	chr14:72462557-73150701	Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12883063	PCNX	cis	cerebellum	SCAN
rs12883063	MED6	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:72470800-72474200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr14:72472800-72474600	Strong transcription	Cortex derived primary cultured neurospheres	brain

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