Variant report

Variant	rs12364139
Chromosome Location	chr11:15892588-15892589
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	chr11:15891804..15893918-chr11:15903502..15905897,2	K562	blood:
2	chr11:15891343..15894307-chr11:16628569..16630598,2	K562	blood:

Variant related genes	Relation type
ENSG00000110693	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10766289	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10766290	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10832526	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11023747	0.85[EUR][1000 genomes]
rs11023753	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11023757	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11023763	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11023766	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12270494	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12270765	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12287547	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12289250	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12290232	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1440705	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1440707	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1866820	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2002372	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2008923	0.83[AMR][1000 genomes]
rs2119376	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2218204	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2615023	0.83[AMR][1000 genomes]
rs2615024	0.83[AMR][1000 genomes]
rs4756835	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4756836	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4756837	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4757370	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4757371	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4757373	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4757374	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4757375	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7106197	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7122245	0.82[AMR][1000 genomes]
rs7481566	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs965476	0.83[AMR][1000 genomes]
rs982988	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[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	nsv832073	chr11:15822409-15984078	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12364139	DKK3	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:15886800-15892600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr11:15887400-15892600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr11:15887400-15892800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr11:15890400-15897000	Weak transcription	Fetal Intestine Small	intestine
5	chr11:15891800-15894600	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr11:15892000-15894000	Enhancers	Brain Germinal Matrix	brain
7	chr11:15892000-15894800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr11:15892200-15893800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr11:15892200-15893800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr11:15892400-15893200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr11:15892400-15894200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr11:15892400-15894400	Enhancers	iPS-18 Cell Line	embryonic stem cell

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