Variant report

Variant	rs9938717
Chromosome Location	chr16:69556506-69556507
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:69555230..69558734-chr16:69596877..69599308,3	K562	blood:
2	chr16:69546010..69548545-chr16:69554522..69557315,2	K562	blood:
3	chr16:69555075..69556617-chr16:69599347..69601386,2	K562	blood:
4	chr16:69554984..69557570-chr16:69599463..69601057,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000102908	Chromatin interaction
ENSG00000223109	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10517	0.95[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap]
rs12102305	0.83[EUR][1000 genomes]
rs13329844	0.91[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap]
rs13335277	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13335317	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13338560	0.85[EUR][1000 genomes]
rs16958965	0.83[EUR][1000 genomes]
rs16958997	0.91[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes]
rs16959059	0.95[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap]
rs2304526	0.91[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.85[TSI][hapmap]
rs28392989	0.81[EUR][1000 genomes]
rs28473508	0.85[EUR][1000 genomes]
rs28637633	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2965753	0.91[CHB][hapmap];0.92[CHD][hapmap];0.88[JPT][hapmap]
rs2965757	0.85[CHB][hapmap]
rs3785075	0.91[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap]
rs3826153	0.85[CHB][hapmap];0.82[CHD][hapmap]
rs3826154	0.95[CHB][hapmap];0.93[CHD][hapmap];0.88[JPT][hapmap];0.89[TSI][hapmap]
rs3926183	0.81[EUR][1000 genomes]
rs60032561	0.87[ASN][1000 genomes]
rs61628167	0.83[EUR][1000 genomes]
rs689452	0.95[CHB][hapmap];0.88[JPT][hapmap]
rs7359387	0.95[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap]
rs889400	0.82[CHB][hapmap]
rs9888993	0.91[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap];0.89[TSI][hapmap]
rs9889219	0.82[CHB][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap]
rs9921652	0.85[CHB][hapmap];0.85[CHD][hapmap]
rs9924264	0.81[EUR][1000 genomes]
rs9924271	0.85[CHB][hapmap];0.85[CHD][hapmap]
rs9924953	0.91[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap];0.89[TSI][hapmap]
rs9925037	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]
rs9934681	0.91[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];0.89[TSI][hapmap]
rs9936464	0.91[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes]
rs9937018	0.90[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431514	chr16:69428599-69581699	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv906821	chr16:69509506-69576894	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9938717	NRN1L	cis	cerebellum	SCAN
rs9938717	HYDIN	cis	parietal	SCAN
rs9938717	NQO1	cis	multi-tissue	Pritchard

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:69548200-69563000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr16:69548600-69556600	Weak transcription	K562	blood
3	chr16:69549200-69560000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr16:69549600-69563200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr16:69550000-69557000	Weak transcription	Placenta	Placenta
6	chr16:69552400-69563200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr16:69554200-69556800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr16:69554600-69557000	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr16:69555400-69561000	Weak transcription	A549	lung
10	chr16:69555600-69562600	Weak transcription	Hela-S3	cervix
11	chr16:69555800-69557200	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr16:69555800-69558400	Enhancers	HepG2	liver
13	chr16:69555800-69560800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr16:69555800-69561200	Weak transcription	HSMM	muscle
15	chr16:69555800-69563200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr16:69555800-69563600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr16:69556200-69556800	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr16:69556200-69563000	Weak transcription	NHEK	skin
19	chr16:69556200-69563200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr16:69556200-69563600	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr16:69556400-69556600	Weak transcription	GM12878-XiMat	blood
22	chr16:69556400-69556800	Active TSS	ES-I3 Cell Line	embryonic stem cell
23	chr16:69556400-69557000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr16:69556400-69557200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr16:69556400-69560800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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