Variant report

Variant	rs9929720
Chromosome Location	chr16:69557096-69557097
allele	C/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	chr16:69554984..69557570-chr16:69599463..69601057,2	MCF-7	breast:
4	chr16:69553013..69554561-chr16:69556746..69558341,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000223109	Chromatin interaction
ENSG00000102908	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10454066	1.00[CEU][hapmap];0.84[CHD][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap]
rs10500551	1.00[CEU][hapmap];0.84[CHD][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap]
rs10852458	1.00[CEU][hapmap]
rs11075728	1.00[CEU][hapmap]
rs11075730	0.84[CHD][hapmap];0.82[MEX][hapmap]
rs11639947	1.00[CEU][hapmap];0.84[CHD][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap]
rs11641233	1.00[CEU][hapmap];0.84[CHD][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap]
rs11642030	1.00[CEU][hapmap]
rs12232410	0.95[CEU][hapmap];0.84[CHD][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap]
rs12447326	0.84[CHD][hapmap];0.82[MEX][hapmap]
rs12595869	1.00[CEU][hapmap];0.84[CHD][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]
rs12596731	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12596823	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs12597243	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12599648	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16958970	1.00[CEU][hapmap];0.84[CHD][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]
rs16959025	1.00[CEU][hapmap];0.85[TSI][hapmap]
rs1800566	1.00[CEU][hapmap];0.84[CHD][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]
rs2161631	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2361838	1.00[CEU][hapmap];0.84[CHD][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap]
rs3169315	1.00[CEU][hapmap];0.84[CHD][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap]
rs3743673	1.00[CEU][hapmap]
rs56256040	0.92[EUR][1000 genomes]
rs60099379	0.83[EUR][1000 genomes]
rs7187653	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7194753	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.94[TSI][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7196943	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs7197614	0.87[ASN][1000 genomes]
rs7198242	1.00[CEU][hapmap];0.84[CHD][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]
rs7200935	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72799376	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs8045705	0.83[EUR][1000 genomes]
rs8046314	1.00[CEU][hapmap]
rs920191	0.82[CHD][hapmap]
rs9788837	1.00[CEU][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]
rs9921045	1.00[CEU][hapmap];0.82[CHD][hapmap];0.91[MEX][hapmap];0.91[TSI][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9929720	LOC440348	cis	multi-tissue	Pritchard
rs9929720	NRN1L	cis	cerebellum	SCAN
rs9929720	CES8	cis	cerebellum	SCAN
rs9929720	LOC440348	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:24 , 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	chr16:69549200-69560000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr16:69549600-69563200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr16:69552400-69563200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr16:69555400-69561000	Weak transcription	A549	lung
6	chr16:69555600-69562600	Weak transcription	Hela-S3	cervix
7	chr16:69555800-69557200	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr16:69555800-69558400	Enhancers	HepG2	liver
9	chr16:69555800-69560800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr16:69555800-69561200	Weak transcription	HSMM	muscle
11	chr16:69555800-69563200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr16:69555800-69563600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr16:69556200-69563000	Weak transcription	NHEK	skin
14	chr16:69556200-69563200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr16:69556200-69563600	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr16:69556400-69557200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr16:69556400-69560800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr16:69556800-69557200	Enhancers	Rectal Mucosa Donor 29	rectum
19	chr16:69556800-69557200	Enhancers	K562	blood
20	chr16:69556800-69563200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr16:69557000-69557400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr16:69557000-69557800	Enhancers	Duodenum Mucosa	Duodenum
23	chr16:69557000-69558000	Enhancers	Placenta	Placenta
24	chr16:69557000-69560400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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