Variant report

Variant	rs2806947
Chromosome Location	chr13:53768025-53768026
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	chr13:53766887..53769388-chr13:53770442..53772910,2	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs12860317	0.85[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap]
rs1322948	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1322953	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1322954	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1322955	0.82[EUR][1000 genomes]
rs1322960	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1407688	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1407689	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1885767	0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1909650	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1923770	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1923772	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1951724	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1951725	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2004422	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2038647	0.86[EUR][1000 genomes]
rs2038648	0.91[ASN][1000 genomes]
rs2181389	0.89[EUR][1000 genomes]
rs2759674	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2759694	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2759698	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2759700	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2759713	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2759714	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2806936	0.81[EUR][1000 genomes]
rs2806937	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2806940	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2806941	0.81[EUR][1000 genomes]
rs2806965	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2806968	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4886312	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5008125	0.82[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	nsv1050969	chr13:53665927-54064861	Bivalent Enhancer Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2806947	NEK5	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:53766000-53771400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr13:53766200-53770800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr13:53766400-53774200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr13:53766600-53770400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr13:53766600-53770800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr13:53767400-53770400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr13:53767400-53771800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr13:53767400-53772000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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