Variant report

Variant	rs12470478
Chromosome Location	chr2:63769308-63769309
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10164844	0.81[JPT][hapmap]
rs10171190	0.86[JPT][hapmap]
rs10200146	0.81[JPT][hapmap]
rs10209490	0.86[JPT][hapmap]
rs1022351	0.86[JPT][hapmap]
rs1022353	0.86[JPT][hapmap]
rs10496102	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1109027	1.00[ASW][hapmap];0.89[CEU][hapmap];0.94[GIH][hapmap];0.94[MEX][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12463603	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12464471	0.89[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12472865	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	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12478365	0.81[ASN][1000 genomes]
rs13409031	0.86[JPT][hapmap]
rs13422170	0.86[JPT][hapmap]
rs17617855	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17618045	1.00[ASW][hapmap];0.89[CEU][hapmap];0.94[GIH][hapmap];0.94[MEX][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17618390	0.81[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs17619012	0.80[EUR][1000 genomes]
rs2138791	0.86[JPT][hapmap]
rs2178678	0.86[JPT][hapmap]
rs2278718	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2421891	0.93[JPT][hapmap]
rs2421892	0.86[JPT][hapmap]
rs2422008	0.86[JPT][hapmap]
rs4567921	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4671061	0.86[JPT][hapmap]
rs4671062	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4671522	0.91[AFR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56219461	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6731136	0.81[JPT][hapmap]
rs6735907	0.86[JPT][hapmap]
rs72806004	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72806010	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72806027	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72806055	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72806056	0.83[EUR][1000 genomes]
rs72806058	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72806082	0.86[EUR][1000 genomes]
rs72806089	0.84[EUR][1000 genomes]
rs72821624	0.93[ASN][1000 genomes]
rs72821628	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72821630	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72821631	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72821632	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12470478	CCT4	cis	parietal	SCAN

Chromatin state (count:3 , 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	chr2:63769200-63769600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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