Variant report

Variant	rs12148043
Chromosome Location	chr14:72472427-72472428
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	chr14:72471348..72475296-chr14:72476061..72479631,3	MCF-7	breast:

Extended variants
information (count: 58 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1009017	1.00[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];0.91[ASN][1000 genomes]
rs11158920	1.00[CEU][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes]
rs11158921	1.00[CEU][hapmap];0.87[CHB][hapmap]
rs11158926	0.88[JPT][hapmap]
rs11158927	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11620690	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11622507	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11623492	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11623535	0.93[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs11625937	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11627768	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11628133	1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11628574	1.00[CEU][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12433721	1.00[CEU][hapmap];0.88[JPT][hapmap]
rs1476745	0.88[JPT][hapmap]
rs17093750	1.00[CEU][hapmap];0.83[JPT][hapmap];0.82[EUR][1000 genomes]
rs17105346	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17105566	1.00[CEU][hapmap];0.93[CHB][hapmap];0.88[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17105606	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17105690	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17768361	0.88[JPT][hapmap]
rs1987722	0.90[ASN][1000 genomes]
rs1987723	0.89[ASN][1000 genomes]
rs2010846	0.90[ASN][1000 genomes]
rs2010850	0.90[ASN][1000 genomes]
rs2052015	0.94[JPT][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2067856	1.00[CEU][hapmap];0.87[CHB][hapmap];0.82[CHD][hapmap];0.89[MEX][hapmap]
rs2159457	1.00[CEU][hapmap]
rs2190864	0.82[JPT][hapmap]
rs2238277	1.00[CEU][hapmap];0.87[CHB][hapmap];0.82[CHD][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs2238280	0.87[CHB][hapmap];0.82[CHD][hapmap]
rs2332705	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3784055	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.82[CHD][hapmap];0.82[GIH][hapmap];0.88[JPT][hapmap];0.94[MEX][hapmap];0.82[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3784056	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.82[CHD][hapmap];0.82[GIH][hapmap];0.88[JPT][hapmap];0.94[MEX][hapmap];0.82[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3784058	1.00[CEU][hapmap];0.88[JPT][hapmap]
rs4243640	0.93[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs4350510	0.93[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs4354860	0.93[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs4899409	1.00[CEU][hapmap];0.87[CHB][hapmap];0.82[CHD][hapmap];0.89[MEX][hapmap];0.82[EUR][1000 genomes]
rs4899412	0.93[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap]
rs4902958	1.00[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes]
rs4902966	0.93[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs56743778	0.82[EUR][1000 genomes]
rs58890880	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59631889	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60503142	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs699358	0.90[ASN][1000 genomes]
rs72734102	0.81[EUR][1000 genomes]
rs72735921	0.82[EUR][1000 genomes]
rs72735923	0.82[EUR][1000 genomes]
rs72735952	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72735955	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72735956	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs728497	1.00[CEU][hapmap];0.87[CHB][hapmap];0.82[CHD][hapmap];0.84[MEX][hapmap]
rs7494103	1.00[CEU][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8013467	0.93[CHB][hapmap];0.93[CHD][hapmap];0.94[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	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12148043	ADAM20	cis	cerebellum	SCAN
rs12148043	MPP5	cis	cerebellum	SCAN
rs12148043	PCNX	cis	cerebellum	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	chr14:72471000-72472800	Weak transcription	Cortex derived primary cultured neurospheres	brain

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