Variant report

Variant	rs9925037
Chromosome Location	chr16:69587212-69587213
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	chr16:69585478..69590758-chr16:69596695..69601394,7	MCF-7	breast:
2	chr16:69585327..69588068-chr16:69597880..69600088,2	K562	blood:

Variant related genes	Relation type
ENSG00000102908	Chromatin interaction
ENSG00000223109	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10517	0.81[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.83[YRI][hapmap]
rs12102305	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13329844	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13335277	0.90[EUR][1000 genomes]
rs13335317	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13338560	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16958965	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16958997	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16959059	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];1.00[YRI][hapmap]
rs2304526	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28392989	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28473508	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28637633	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2917667	0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.96[LWK][hapmap];0.85[MEX][hapmap];1.00[YRI][hapmap]
rs2917669	0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap]
rs2917681	1.00[YRI][hapmap]
rs2917682	0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.83[LWK][hapmap];1.00[YRI][hapmap]
rs2917683	0.90[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs2965753	0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];1.00[YRI][hapmap]
rs2965757	0.90[CHB][hapmap]
rs3785075	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs3826153	0.90[CHB][hapmap];0.90[CHD][hapmap];0.83[JPT][hapmap]
rs3826154	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs3926183	0.91[AFR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61628167	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6499249	0.84[CHD][hapmap];0.88[LWK][hapmap];0.80[MKK][hapmap];1.00[YRI][hapmap]
rs689452	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs7200420	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7359387	1.00[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap]
rs9888993	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs9889219	0.86[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap]
rs9921652	0.90[CHB][hapmap];0.93[CHD][hapmap];0.83[JPT][hapmap]
rs9924264	0.91[AFR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9924271	0.90[CHB][hapmap];0.93[CHD][hapmap];0.83[JPT][hapmap]
rs9924953	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.96[LWK][hapmap];0.85[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap]
rs9927809	0.84[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs9934321	0.84[AFR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9934681	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs9936464	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9937018	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9938717	0.91[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes];0.82[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	nsv1852	chr16:69566121-69610962	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9925037	NOL3	cis	cerebellum	SCAN
rs9925037	NRN1L	cis	cerebellum	SCAN
rs9925037	NQO1	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:69574600-69597800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr16:69587000-69587600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr16:69587000-69587600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr16:69587200-69587600	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr16:69587200-69587600	Enhancers	Primary hematopoietic stem cells	blood
6	chr16:69587200-69587800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr16:69587200-69588000	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr16:69587200-69589400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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