Variant report

Variant	rs1008578
Chromosome Location	chr12:4709450-4709451
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	chr12:4709411..4711345-chr12:4712609..4715174,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000010219	Chromatin interaction
ENSG00000272921	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10744653	0.92[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10744654	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10774245	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11063253	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12303320	0.91[CEU][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12313377	0.89[EUR][1000 genomes]
rs12828416	0.93[CEU][hapmap];0.91[EUR][1000 genomes]
rs1860343	0.96[CEU][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1860344	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1974602	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2041293	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2286576	0.85[CEU][hapmap];0.90[EUR][1000 genomes]
rs2299833	0.90[EUR][1000 genomes]
rs2302248	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2884671	0.91[EUR][1000 genomes]
rs35131771	0.92[EUR][1000 genomes]
rs4766260	0.90[CEU][hapmap];0.86[EUR][1000 genomes]
rs7136668	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs720673	0.82[EUR][1000 genomes]
rs7300543	0.92[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs730065	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7305150	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7972737	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs7975484	0.93[CEU][hapmap];0.92[EUR][1000 genomes]
rs7977981	0.92[CEU][hapmap];0.92[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	nsv557123	chr12:4436632-4736569	Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv832318	chr12:4655799-4875837	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1008578	DYRK4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:4704000-4713200	Strong transcription	Primary neutrophils fromperipheralblood	blood
2	chr12:4709000-4713800	Weak transcription	Primary B cells from cord blood	blood
3	chr12:4709400-4713800	Weak transcription	Primary B cells from peripheral blood	blood

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