Variant report

Variant	rs13334887
Chromosome Location	chr16:81047178-81047179
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:81047118-81047253	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr16:81047033-81047290	HepG2	liver:	n/a	n/a
3	POLR2A	chr16:81046880-81047373	K562	blood:	n/a	n/a
4	POLR2A	chr16:81046885-81047455	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:81045576..81047236-chr16:81766244..81767798,2	K562	blood:
2	chr16:81047016..81048969-chr16:81058785..81061103,3	MCF-7	breast:
3	chr16:81045256..81047654-chr16:81067599..81069498,2	MCF-7	breast:

Variant related genes	Relation type
CENPN	TF binding region
ENSG00000260213	Chromatin interaction
ENSG00000166454	Chromatin interaction

Extended variants
information (count: 142 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:133)

rs_ID	r²[population]
rs11150333	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11150334	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1127390	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11866375	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11866803	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12446304	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12446810	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12448656	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13331118	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13332890	0.88[EUR][1000 genomes]
rs13332902	0.88[EUR][1000 genomes]
rs13336292	0.88[EUR][1000 genomes]
rs13336629	0.88[EUR][1000 genomes]
rs1453327	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1453328	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1469123	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1469124	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1469125	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1469126	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1477381	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16944339	0.82[ASN][1000 genomes]
rs16944345	0.84[ASN][1000 genomes]
rs1964298	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2018122	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2098726	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2113196	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2113197	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2123627	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2167889	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2194321	0.88[ASN][1000 genomes]
rs2194322	0.84[ASN][1000 genomes]
rs2216753	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2244452	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2287991	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2316923	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2549828	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2549833	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2549835	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2549836	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2549837	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2549838	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2549839	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2549840	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2549841	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2549842	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2549843	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2549844	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2549846	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2549847	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2549848	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2549852	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2549853	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2549854	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2549855	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2549856	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2549857	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2549858	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2549859	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2549861	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2549863	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2549865	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2549866	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2549867	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2549868	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2549869	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2549870	0.88[ASN][1000 genomes]
rs2549871	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2549872	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2549879	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2549883	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2549886	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2549887	0.94[EUR][1000 genomes]
rs2549888	0.94[EUR][1000 genomes]
rs2602409	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2602410	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2602411	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2602412	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2602413	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2602414	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2602416	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2602417	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2602418	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2602419	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2602423	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2602424	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2602426	0.94[EUR][1000 genomes]
rs2602433	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2602434	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2602435	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2602436	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2602437	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2602440	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2602441	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2602443	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2602446	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2602448	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2602449	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2602453	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2911148	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2911149	0.83[ASN][1000 genomes]
rs2911150	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2911151	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2970079	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2970081	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2970083	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2970084	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2970085	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2970086	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3112035	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3112036	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3784814	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3826048	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55776427	0.90[EUR][1000 genomes]
rs56306230	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60779117	0.90[ASN][1000 genomes]
rs6564814	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs66516157	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71400133	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7196960	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs874053	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs874054	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9888895	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9889194	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9921448	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9921914	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9923948	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9925780	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9931292	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9932857	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9934957	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9936366	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9937731	0.90[EUR][1000 genomes]
rs9938541	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948534	chr16:80867635-81160492	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1065258	chr16:80887483-81081768	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer 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 miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv1058045	chr16:80918138-81048242	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	nsv1064164	chr16:80918138-81126967	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
5	nsv542991	chr16:80918138-81126967	Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
6	nsv532569	chr16:80980356-81700149	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
7	nsv532597	chr16:81009718-81388348	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
8	nsv573338	chr16:81020393-81106944	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
9	nsv427984	chr16:81026691-81320341	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13334887	CENPN	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:81041600-81047600	Weak transcription	Spleen	Spleen
2	chr16:81041800-81053600	Weak transcription	Gastric	stomach
3	chr16:81041800-81069000	Weak transcription	Ovary	ovary
4	chr16:81041800-81069000	Weak transcription	Small Intestine	intestine
5	chr16:81042000-81047400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr16:81042000-81047800	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr16:81042000-81047800	Weak transcription	Aorta	Aorta
8	chr16:81042000-81047800	Weak transcription	Right Ventricle	heart
9	chr16:81042000-81048000	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr16:81042000-81048200	Weak transcription	Brain Cingulate Gyrus	brain
11	chr16:81042000-81048200	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr16:81042000-81053000	Weak transcription	Brain Angular Gyrus	brain
13	chr16:81042000-81053600	Weak transcription	HSMMtube	muscle
14	chr16:81042000-81054400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr16:81042000-81054800	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr16:81042000-81057600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr16:81042000-81058400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr16:81042000-81069000	Weak transcription	Esophagus	oesophagus
19	chr16:81042000-81069000	Weak transcription	Pancreas	Pancrea
20	chr16:81042000-81069600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr16:81042200-81047400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr16:81042200-81047600	Weak transcription	Fetal Brain Female	brain
23	chr16:81042200-81047800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr16:81042200-81047800	Weak transcription	Primary B cells from peripheral blood	blood
25	chr16:81042200-81047800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr16:81042200-81048200	Weak transcription	Brain Anterior Caudate	brain
27	chr16:81042200-81052200	Weak transcription	Stomach Smooth Muscle	stomach
28	chr16:81042200-81053600	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr16:81042200-81058600	Weak transcription	Rectal Smooth Muscle	rectum
30	chr16:81042200-81068800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr16:81042200-81069000	Weak transcription	Colonic Mucosa	Colon
32	chr16:81042200-81069600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr16:81042400-81047600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr16:81042400-81047600	Weak transcription	Lung	lung
35	chr16:81042400-81049600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr16:81042400-81052400	Weak transcription	Brain Hippocampus Middle	brain
37	chr16:81042400-81056200	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr16:81042400-81069000	Weak transcription	Brain Germinal Matrix	brain
39	chr16:81042400-81069000	Weak transcription	Fetal Heart	heart
40	chr16:81042600-81064200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr16:81043000-81059200	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr16:81043000-81063800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr16:81043000-81064600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr16:81043000-81065400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr16:81043200-81062800	Strong transcription	K562	blood
46	chr16:81043200-81065200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
47	chr16:81043400-81058800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
48	chr16:81044000-81055600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr16:81044000-81057400	Strong transcription	HepG2	liver
50	chr16:81044000-81064400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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