Variant report

Variant	rs2759714
Chromosome Location	chr13:53763753-53763754
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:53542220..53542850-chr13:53763028..53763897,2	MCF-7	breast:
2	chr13:53593128..53594726-chr13:53763262..53764959,2	MCF-7	breast:
3	chr13:53762930..53764777-chr13:53766353..53768013,2	K562	blood:
4	chr13:53578448..53579351-chr13:53763194..53763965,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs12860317	0.85[CEU][hapmap]
rs1322948	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1322953	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1322954	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1322955	0.82[EUR][1000 genomes]
rs1322960	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1407688	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1407689	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1885767	0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1909650	0.93[JPT][hapmap]
rs1923770	0.80[EUR][1000 genomes]
rs1923772	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1951724	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1951725	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2004422	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2038647	0.86[EUR][1000 genomes]
rs2181389	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2759674	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2759694	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2759698	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2759700	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2759713	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2806936	0.81[EUR][1000 genomes]
rs2806937	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2806940	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2806941	0.81[EUR][1000 genomes]
rs2806947	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2806965	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2806968	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4886312	0.85[EUR][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
rs2759714	NEK5	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:53761800-53764000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr13:53762600-53765200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr13:53762600-53767400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr13:53763000-53763800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr13:53763000-53764200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr13:53763400-53763800	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr13:53763400-53767400	Enhancers	Placenta Amnion	Placenta Amnion
8	chr13:53763600-53764400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr13:53763600-53765600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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