Variant report

Variant	rs7428097
Chromosome Location	chr3:54345400-54345401
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	chr3:54180345..54181406-chr3:54345179..54346094,3	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs12374075	0.86[CHB][hapmap]
rs12374128	0.86[CHB][hapmap]
rs3934633	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4078006	0.88[YRI][hapmap]
rs4078007	0.88[YRI][hapmap]
rs41277447	0.94[EUR][1000 genomes]
rs55715726	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55768606	0.86[ASN][1000 genomes]
rs55826666	0.86[ASN][1000 genomes]
rs55982339	0.86[ASN][1000 genomes]
rs56212431	0.86[ASN][1000 genomes]
rs56305246	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56411589	0.86[ASN][1000 genomes]
rs57211759	0.86[ASN][1000 genomes]
rs57711599	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60921965	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61027914	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61566355	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62254144	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62254145	0.90[ASN][1000 genomes]
rs62254148	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62254149	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62254159	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62256061	0.93[EUR][1000 genomes]
rs62256085	0.93[EUR][1000 genomes]
rs62256091	0.94[EUR][1000 genomes]
rs62256099	0.93[EUR][1000 genomes]
rs6445640	0.87[ASN][1000 genomes]
rs6445646	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs6769262	0.94[EUR][1000 genomes]
rs6781457	0.88[YRI][hapmap]
rs6790114	0.88[YRI][hapmap]
rs6807491	0.90[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs6810291	0.86[EUR][1000 genomes]
rs7426971	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs7434141	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7635568	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7645884	0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1014595	chr3:53944473-54846754	Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv817328	chr3:54250314-54380438	Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7428097	NEK4	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54338400-54345400	Weak transcription	Fetal Lung	lung
2	chr3:54344000-54347600	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr3:54344000-54360800	Weak transcription	Psoas Muscle	Psoas
4	chr3:54345000-54345600	Enhancers	Right Atrium	heart
5	chr3:54345200-54347600	Enhancers	Fetal Brain Male	brain
6	chr3:54345400-54345600	Enhancers	Ovary	ovary
7	chr3:54345400-54346800	Enhancers	Fetal Stomach	stomach
8	chr3:54345400-54347400	Enhancers	Fetal Lung	lung

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