Variant report

Variant	rs12472865
Chromosome Location	chr2:63771769-63771770
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:63715008..63715919-chr2:63770832..63771824,3	MCF-7	breast:

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10496102	0.84[CEU][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs1109027	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12463603	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12464471	1.00[YRI][hapmap]
rs12470478	1.00[ASW][hapmap];0.89[CEU][hapmap];0.88[GIH][hapmap];0.88[MEX][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12476015	0.82[EUR][1000 genomes]
rs17617855	0.82[EUR][1000 genomes]
rs17618045	1.00[ASW][hapmap];1.00[CEU][hapmap];0.80[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17618390	1.00[YRI][hapmap]
rs17619012	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2054120	0.83[EUR][1000 genomes]
rs2278718	0.84[CEU][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs4671062	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72806004	0.82[EUR][1000 genomes]
rs72806010	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72806027	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72806056	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72821628	0.80[EUR][1000 genomes]
rs72821630	0.80[EUR][1000 genomes]
rs72821631	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72821632	0.80[AMR][1000 genomes];0.85[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	esv1800788	chr2:63473443-63900292	ZNF genes & repeats Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12472865	CCT4	cis	parietal	SCAN
rs12472865	GNAO1	trans	lymphoblastoid	RTeQTL

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:63766800-63773600	Weak transcription	Left Ventricle	heart
2	chr2:63768600-63777400	Weak transcription	Primary hematopoietic stem cells	blood
3	chr2:63771200-63772600	Enhancers	iPS-18 Cell Line	embryonic stem cell
4	chr2:63771200-63773200	Enhancers	HUES48 Cell Line	embryonic stem cell

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