Variant report

Variant	rs13333122
Chromosome Location	chr16:72654326-72654327
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	chr16:72653301..72655444-chr16:72697417..72699415,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261008	Chromatin interaction
ENSG00000259768	Chromatin interaction

Extended variants
information (count: 134 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:118)

rs_ID	r²[population]
rs1001493	0.85[EUR][1000 genomes]
rs1006805	0.87[EUR][1000 genomes]
rs10468266	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10492821	0.83[EUR][1000 genomes]
rs11641842	0.90[EUR][1000 genomes]
rs11643203	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11860023	0.86[EUR][1000 genomes]
rs12051542	0.90[EUR][1000 genomes]
rs12325146	0.91[EUR][1000 genomes]
rs12325151	0.91[EUR][1000 genomes]
rs12445443	0.87[EUR][1000 genomes]
rs12596611	0.86[EUR][1000 genomes]
rs12599375	0.89[EUR][1000 genomes]
rs12708933	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs13335806	0.86[EUR][1000 genomes]
rs1429072	0.89[EUR][1000 genomes]
rs1560278	0.91[EUR][1000 genomes]
rs16971030	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16971035	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16971036	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16971037	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16971050	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16971112	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16971114	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17287903	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17359949	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17608557	0.83[CEU][hapmap]
rs17609544	0.91[EUR][1000 genomes]
rs17609577	0.91[EUR][1000 genomes]
rs17609787	0.93[EUR][1000 genomes]
rs17609808	0.93[EUR][1000 genomes]
rs17677484	0.93[EUR][1000 genomes]
rs17677616	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[EUR][1000 genomes]
rs17677890	0.93[EUR][1000 genomes]
rs17841357	0.88[EUR][1000 genomes]
rs1864229	0.85[EUR][1000 genomes]
rs2163068	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2358801	0.86[EUR][1000 genomes]
rs2905697	0.89[EUR][1000 genomes]
rs2905699	0.92[EUR][1000 genomes]
rs2914774	0.89[EUR][1000 genomes]
rs2914777	0.87[EUR][1000 genomes]
rs2914779	0.91[EUR][1000 genomes]
rs2967232	0.92[EUR][1000 genomes]
rs2967233	0.88[EUR][1000 genomes]
rs2967234	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs2967240	0.85[EUR][1000 genomes]
rs35005335	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4788473	0.91[EUR][1000 genomes]
rs4788646	0.81[EUR][1000 genomes]
rs55766519	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55808336	0.93[EUR][1000 genomes]
rs56323671	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56347149	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56348767	0.95[EUR][1000 genomes]
rs56389222	0.92[EUR][1000 genomes]
rs56404261	0.86[EUR][1000 genomes]
rs57220817	0.93[EUR][1000 genomes]
rs58549165	0.93[EUR][1000 genomes]
rs58745414	0.93[EUR][1000 genomes]
rs58770834	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58860566	0.91[EUR][1000 genomes]
rs60502114	0.91[EUR][1000 genomes]
rs61475520	0.91[EUR][1000 genomes]
rs62051486	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62051488	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62051497	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62051500	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62052877	0.91[EUR][1000 genomes]
rs62052878	0.90[EUR][1000 genomes]
rs62052879	0.91[EUR][1000 genomes]
rs62052880	0.87[EUR][1000 genomes]
rs62052881	0.91[EUR][1000 genomes]
rs62052888	0.91[EUR][1000 genomes]
rs62052890	0.93[EUR][1000 genomes]
rs62052891	0.93[EUR][1000 genomes]
rs62052894	0.84[EUR][1000 genomes]
rs62052895	0.93[EUR][1000 genomes]
rs62052909	0.93[EUR][1000 genomes]
rs62052911	0.93[EUR][1000 genomes]
rs62052915	0.91[EUR][1000 genomes]
rs62052920	0.93[EUR][1000 genomes]
rs62052921	0.93[EUR][1000 genomes]
rs62052923	0.86[EUR][1000 genomes]
rs62052927	0.95[EUR][1000 genomes]
rs62052954	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62054469	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62054470	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7188640	0.90[EUR][1000 genomes]
rs7189331	0.91[EUR][1000 genomes]
rs7192221	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7193177	0.93[EUR][1000 genomes]
rs7194470	0.86[EUR][1000 genomes]
rs7198233	0.88[EUR][1000 genomes]
rs7198431	0.89[EUR][1000 genomes]
rs7198788	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7199970	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7205109	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs72793252	0.91[EUR][1000 genomes]
rs72793263	0.95[EUR][1000 genomes]
rs72793266	0.93[EUR][1000 genomes]
rs72793271	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72803199	0.87[ASN][1000 genomes]
rs8044665	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8046749	0.89[EUR][1000 genomes]
rs8048181	0.84[EUR][1000 genomes]
rs8048832	1.00[CEU][hapmap];0.97[GIH][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs8049577	0.89[EUR][1000 genomes]
rs8050815	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8059626	0.82[EUR][1000 genomes]
rs8064129	0.86[EUR][1000 genomes]
rs877641	0.86[EUR][1000 genomes]
rs9922217	0.86[EUR][1000 genomes]
rs9924296	0.86[EUR][1000 genomes]
rs9925470	0.81[EUR][1000 genomes]
rs9940600	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs999697	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs999698	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1060983	chr16:72074832-72791629	Genic enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
2	nsv1060804	chr16:72078486-72791629	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
3	nsv534039	chr16:72287171-72851170	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv530712	chr16:72499171-72744114	Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv1065173	chr16:72509626-72693970	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv542951	chr16:72509626-72693970	Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv1064027	chr16:72559417-72656702	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv1063049	chr16:72577004-72887111	Weak transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
9	nsv542952	chr16:72577004-72887111	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
10	nsv1056987	chr16:72620573-72658730	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv1064112	chr16:72620573-72671503	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv1066815	chr16:72627782-72658730	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv1055808	chr16:72627782-72667298	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	nsv431515	chr16:72633299-72654499	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
15	esv1818026	chr16:72633305-72704680	Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
16	nsv1059111	chr16:72647569-72751907	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13333122	PRMT7	cis	cerebellum	SCAN
rs13333122	PSMB10	cis	cerebellum	SCAN
rs13333122	NRN1L	cis	cerebellum	SCAN
rs13333122	DHODH	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:72643600-72660600	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr16:72644400-72660400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr16:72646600-72659600	Weak transcription	HepG2	liver
4	chr16:72649600-72659600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr16:72650400-72654600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr16:72651400-72654400	Weak transcription	Primary B cells from cord blood	blood

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